7-123131653-C-T

Variant names:

• chr7-123131653-C-T
• rs1320393
• NM_022444.4:c.933-2172G>A

Variant summary

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

The NM_022444.4(SLC13A1):​c.933-2172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,910 control chromosomes in the GnomAD database, including 27,955 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 0.60 (27955 hom., cov: 31)
• Consequence: SLC13A1 NM_022444.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 3 publications found

Genes affected

SLC13A1 (HGNC:10916): (solute carrier family 13 member 1) The protein encoded by this gene is an apical membrane Na(+)-sulfate cotransporter involved in sulfate homeostasis in the kidney. Defects in this gene lead to many pathophysiologic problems. [provided by RefSeq, May 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC13A1	NM_022444.4	c.933-2172G>A		intron_variant	Intron 8 of 14	ENST00000194130.7	NP_071889.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC13A1	ENST00000194130.7	c.933-2172G>A		intron_variant	Intron 8 of 14	1	NM_022444.4	ENSP00000194130.2
SLC13A1	ENST00000439260.5	n.*1311-2172G>A		intron_variant	Intron 11 of 17	1		ENSP00000401417.1
SLC13A1	ENST00000539873.1	c.*600-2172G>A		intron_variant	Intron 9 of 15	5		ENSP00000441309.1
SLC13A1	ENST00000427975.5	n.*876-2172G>A		intron_variant	Intron 9 of 15	5		ENSP00000388403.1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91730 AN: 151792 Hom.: 27910 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.605 AC: 91836 AN: 151910 Hom.: 27955 Cov.: 31 AF XY: 0.605 AC XY: 44913 AN XY: 74208

African (AFR) AF: 0.669 AC: 27717 AN: 41428

American (AMR) AF: 0.532 AC: 8110 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1751 AN: 3460

East Asian (EAS) AF: 0.662 AC: 3411 AN: 5154

South Asian (SAS) AF: 0.531 AC: 2554 AN: 4806

European-Finnish (FIN) AF: 0.633 AC: 6677 AN: 10556

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39621 AN: 67932

Other (OTH) AF: 0.603 AC: 1274 AN: 2114

Alfa AF: 0.582 Hom.: 12997

Bravo AF: 0.600

Asia WGS AF: 0.612 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.62
PhyloP100		-0.41
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: rs1320393; hg19: chr7-122771707;