NM_207113.3:c.198+2654T>G

Variant names:

• chr7-140377628-A-C
• rs6955063
• NM_207113.3:c.198+2654T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

SLC37A3 Gene-Disease associations (from GenCC):

• retinitis pigmentosa

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC37A3	NM_207113.3	c.198+2654T>G		intron_variant	Intron 3 of 14	ENST00000326232.14	NP_996996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC37A3	ENST00000326232.14	c.198+2654T>G		intron_variant	Intron 3 of 14	1	NM_207113.3	ENSP00000321498.9

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

African (AFR) AF: 0.302 AC: 12514 AN: 41490

American (AMR) AF: 0.0964 AC: 1473 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.108 AC: 562 AN: 5184

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4822

European-Finnish (FIN) AF: 0.0863 AC: 914 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7073 AN: 68028

Other (OTH) AF: 0.145 AC: 306 AN: 2114

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
PhyloP100		0.049
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: rs6955063; hg19: chr7-140077428;