rs727504456

Variant names:

• chr7-103421426-T-C
• rs727504456
• NM_198999.3:c.89A>G

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP6

The NM_198999.3(SLC26A5):​c.89A>G​(p.Glu30Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: SLC26A5 NM_198999.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.52
• Publications: 1 publications found

Genes affected

SLC26A5 (HGNC:9359): (solute carrier family 26 member 5) This gene encodes a member of the SLC26A/SulP transporter family. The protein functions as a molecular motor in motile outer hair cells (OHCs) of the cochlea, inducing changes in cell length that act to amplify sound levels. The transmembrane protein is an incomplete anion transporter, and does not allow anions to cross the cell membrane but instead undergoes a conformational change in response to changes in intracellular Cl- levels that results in a change in cell length. The protein functions at microsecond rates, which is several orders of magnitude faster than conventional molecular motor proteins. Mutations in this gene are potential candidates for causing neurosensory deafness. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2009]

SLC26A5 Gene-Disease associations (from GenCC):

• autosomal recessive nonsyndromic hearing loss 61

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2153855).
• BP6: Variant 7-103421426-T-C is Benign according to our data. Variant chr7-103421426-T-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 178676.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC26A5	NM_198999.3	c.89A>G	p.Glu30Gly	missense_variant	Exon 3 of 20	ENST00000306312.8	NP_945350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC26A5	ENST00000306312.8	c.89A>G	p.Glu30Gly	missense_variant	Exon 3 of 20	1	NM_198999.3	ENSP00000304783.3
SLC26A5	ENST00000393727.5	c.89A>G	p.Glu30Gly	missense_variant	Exon 1 of 18	1		ENSP00000377328.1
SLC26A5	ENST00000393723.2	c.89A>G	p.Glu30Gly	missense_variant	Exon 1 of 17	1		ENSP00000377324.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000342 AC: 5 AN: 1461790 Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4 AN XY: 727202

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00 AC: 0 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53412

Middle Eastern (MID) AF: 0.000173 AC: 1 AN: 5768

European-Non Finnish (NFE) AF: 0.00000270 AC: 3 AN: 1111934

Other (OTH) AF: 0.0000166 AC: 1 AN: 60390

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 18, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Glu30Gly in exon 3 of SLC26A5: This variant is not expected to have clinical sig nificance because glutamic acid (Glu) at position 30 is not conserved in mammals or evolutionarily distant species and the change to glycine (Gly) is present in wallaby, opposum and chicken. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Uncertain	0.017	T
BayesDel_noAF	Benign	-0.21
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.77	.;.;.;.;D;.;T;.;T;.
Eigen	Benign	-0.27
Eigen_PC	Benign	-0.066
FATHMM_MKL	Benign	0.58	D
LIST_S2	Benign	0.82	T;T;T;.;T;T;T;T;.;T
M_CAP	Uncertain	0.13	D
MetaRNN	Benign	0.22	T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	-0.17	T
MutationAssessor	Benign	0.40	N;N;N;N;N;N;.;.;.;N
PhyloP100		1.5
PrimateAI	Benign	0.43	T
PROVEAN	Uncertain	-3.5	D;D;D;D;D;D;.;D;D;D
REVEL	Benign	0.27
Sift	Benign	0.077	T;T;D;T;T;T;.;T;T;T
Sift4G	Benign	0.12	T;T;T;T;T;T;T;T;T;T
Polyphen		0.0020	B;B;B;.;B;.;.;.;.;.
Vest4		0.18
MutPred		0.45		Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);Gain of catalytic residue at P26 (P = 0.0838);
MVP		0.88
MPC		0.16
ClinPred		0.23	T
GERP RS		4.3
PromoterAI		-0.024	Neutral
Varity_R		0.13
gMVP		0.52
Mutation Taster		=82/18	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs727504456; hg19: chr7-103061873; COSMIC: COSV59704163;