rs12703774

Positions:

• chr7-140351263-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207113.3(SLC37A3):​c.882+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 1,608,512 control chromosomes in the GnomAD database, including 161,070 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 0.41 (13137 hom., cov: 32)
  • Exomes 𝑓: 0.45 (147933 hom.)
• Consequence: SLC37A3 NM_207113.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

SLC37A3 (HGNC:20651): (solute carrier family 37 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in carbohydrate transport and transmembrane transport. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC37A3	NM_207113.3	c.882+10G>A		intron_variant		ENST00000326232.14	NP_996996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC37A3	ENST00000326232.14	c.882+10G>A		intron_variant		1	NM_207113.3	ENSP00000321498	P1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62336 AN: 151954 Hom.: 13137 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.412

GnomAD3 exomes AF: 0.429 AC: 106479 AN: 248216 Hom.: 23011 AF XY: 0.429 AC XY: 57557 AN XY: 134118

Gnomad AFR exome AF: 0.318

Gnomad AMR exome AF: 0.403

Gnomad ASJ exome AF: 0.401

Gnomad EAS exome AF: 0.439

Gnomad SAS exome AF: 0.396

Gnomad FIN exome AF: 0.447

Gnomad NFE exome AF: 0.458

Gnomad OTH exome AF: 0.448

GnomAD4 exome AF: 0.449 AC: 654052 AN: 1456440 Hom.: 147933 Cov.: 35 AF XY: 0.448 AC XY: 324243 AN XY: 724464

Gnomad4 AFR exome AF: 0.321

Gnomad4 AMR exome AF: 0.399

Gnomad4 ASJ exome AF: 0.404

Gnomad4 EAS exome AF: 0.402

Gnomad4 SAS exome AF: 0.394

Gnomad4 FIN exome AF: 0.449

Gnomad4 NFE exome AF: 0.462

Gnomad4 OTH exome AF: 0.444

GnomAD4 genome AF: 0.410 AC: 62369 AN: 152072 Hom.: 13137 Cov.: 32 AF XY: 0.411 AC XY: 30522 AN XY: 74320

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.413

Alfa AF: 0.434 Hom.: 8689

Bravo AF: 0.403

Asia WGS AF: 0.409 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.11
DANN	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs12703774; hg19: chr7-140051063; COSMIC: COSV58263643; COSMIC: COSV58263643;