chr18-45730381-C-G

Variant names:

• chr18-45730381-C-G
• rs765284140
• NM_015865.7:c.61C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015865.7(SLC14A1):​c.61C>G​(p.Gln21Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q21K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC14A1 NM_015865.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• Publications: 1 publications found

Genes affected

SLC14A1 (HGNC:10918): (solute carrier family 14 member 1 (Kidd blood group)) The protein encoded by this gene is a membrane transporter that mediates urea transport in erythrocytes. This gene forms the basis for the Kidd blood group system. [provided by RefSeq, Mar 2009]

ENSG00000288545 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.070275754).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015865.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A1	NM_015865.7	MANE Select	c.61C>G	p.Gln21Glu	missense	Exon 3 of 10	NP_056949.4	Q13336-1
	SLC14A1	NM_001128588.4		c.229C>G	p.Gln77Glu	missense	Exon 4 of 11	NP_001122060.3	Q13336-2
	SLC14A1	NM_001146037.1		c.229C>G	p.Gln77Glu	missense	Exon 2 of 9	NP_001139509.1	Q13336-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC14A1	ENST00000321925.9	TSL:1 MANE Select	c.61C>G	p.Gln21Glu	missense	Exon 3 of 10	ENSP00000318546.4	Q13336-1
	SLC14A1	ENST00000586142.5	TSL:1	c.61C>G	p.Gln21Glu	missense	Exon 1 of 8	ENSP00000470476.1	Q13336-1
	SLC14A1	ENST00000589700.5	TSL:1	c.61C>G	p.Gln21Glu	missense	Exon 1 of 7	ENSP00000465044.1	E9NSU1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.061
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	8.4
DANN	Benign	0.89
DEOGEN2	Benign	0.086	T
Eigen	Benign	-0.64
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.20	N
LIST_S2	Benign	0.63	T
M_CAP	Benign	0.0099	T
MetaRNN	Benign	0.070	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	L
PhyloP100		0.91
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-0.77	N
REVEL	Benign	0.041
Sift	Benign	0.55	T
Sift4G	Benign	0.62	T
Polyphen		0.0	B
Vest4		0.12
MutPred		0.22		Loss of MoRF binding (P = 0.0708)
MVP		0.47
MPC		0.11
ClinPred		0.16	T
GERP RS		3.9
PromoterAI		0.022	Neutral
Varity_R		0.10
gMVP		0.10
Mutation Taster		=86/14	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs765284140; hg19: chr18-43310346;