chr7-140377628-A-C

Position:

• chr7-140377628-A-C

Variant summary

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

The NM_207113.3(SLC37A3):​c.198+2654T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,188 control chromosomes in the GnomAD database, including 2,649 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 0.16 (2649 hom., cov: 32)
• Consequence: SLC37A3 NM_207113.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC37A3	NM_207113.3	c.198+2654T>G		intron_variant		ENST00000326232.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC37A3	ENST00000326232.14	c.198+2654T>G		intron_variant		1	NM_207113.3	P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24447 AN: 152070 Hom.: 2632 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0863

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.161 AC: 24516 AN: 152188 Hom.: 2649 Cov.: 32 AF XY: 0.160 AC XY: 11895 AN XY: 74438

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.0964

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0863

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.145

Alfa AF: 0.135 Hom.: 366

Bravo AF: 0.165

Asia WGS AF: 0.188 AC: 654 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.60

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: rs6955063; hg19: chr7-140077428;