rs7610114

Variant names:

• chr3-27417131-C-T
• rs7610114
• NM_001321103.2:c.1659+1355G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321103.2(SLC4A7):​c.1659+1355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 152,224 control chromosomes in the GnomAD database, including 66,451 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.93 (66451 hom., cov: 31)
• Consequence: SLC4A7 NM_001321103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 0 publications found

Genes affected

SLC4A7 (HGNC:11033): (solute carrier family 4 member 7) This locus encodes a sodium bicarbonate cotransporter. The encoded transmembrane protein appears to transport sodium and bicarbonate ions in a 1:1 ratio, and is thus considered an electroneutral cotransporter. The encoded protein likely plays a critical role in regulation of intracellular pH involved in visual and auditory sensory transmission. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]

SLC4A7 Gene-Disease associations (from GenCC):

• cone-rod dystrophy

  Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321103.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC4A7	NM_001321103.2	MANE Select	c.1659+1355G>A		intron	N/A	NP_001308032.1
	SLC4A7	NM_001321104.2		c.1620+1355G>A		intron	N/A	NP_001308033.1
	SLC4A7	NM_003615.5		c.1632+1355G>A		intron	N/A	NP_003606.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC4A7	ENST00000454389.6	TSL:1 MANE Select	c.1659+1355G>A		intron	N/A	ENSP00000390394.1
	SLC4A7	ENST00000440156.5	TSL:1	c.1620+1355G>A		intron	N/A	ENSP00000414797.1
	SLC4A7	ENST00000295736.9	TSL:1	c.1632+1355G>A		intron	N/A	ENSP00000295736.5

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142029 AN: 152106 Hom.: 66387 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.933

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.934 AC: 142154 AN: 152224 Hom.: 66451 Cov.: 31 AF XY: 0.935 AC XY: 69542 AN XY: 74412

African (AFR) AF: 0.908 AC: 37731 AN: 41532

American (AMR) AF: 0.955 AC: 14601 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3253 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5162 AN: 5164

South Asian (SAS) AF: 0.938 AC: 4524 AN: 4824

European-Finnish (FIN) AF: 0.928 AC: 9839 AN: 10600

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 63985 AN: 68030

Other (OTH) AF: 0.934 AC: 1975 AN: 2114

Alfa AF: 0.935 Hom.: 30567

Bravo AF: 0.934

Asia WGS AF: 0.971 AC: 3377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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: rs7610114; hg19: chr3-27458622;