rs3130713

Variant names:

• chr6-31237840-G-T
• rs3130713

Variant summary

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

The variant allele was found at a frequency of 0.225 in 152,042 control chromosomes in the GnomAD database, including 4,001 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 0.23 (4001 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 10 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34249 AN: 151922 Hom.: 4000 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.225 AC: 34256 AN: 152042 Hom.: 4001 Cov.: 33 AF XY: 0.221 AC XY: 16441 AN XY: 74320

African (AFR) AF: 0.167 AC: 6931 AN: 41490

American (AMR) AF: 0.197 AC: 3006 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3468

East Asian (EAS) AF: 0.283 AC: 1464 AN: 5170

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4824

European-Finnish (FIN) AF: 0.180 AC: 1899 AN: 10544

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18012 AN: 67960

Other (OTH) AF: 0.239 AC: 504 AN: 2110

Alfa AF: 0.239 Hom.: 2544

Bravo AF: 0.223

Asia WGS AF: 0.220 AC: 767 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.33
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3130713; hg19: chr6-31205617;