6-31222526-T-C

Variant names:

• chr6-31222526-T-C
• rs3130517

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 0.288 in 152,182 control chromosomes in the GnomAD database, including 6,429 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 0.29 (6429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.288 AC: 43825 AN: 152062 Hom.: 6425 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.288 AC: 43854 AN: 152182 Hom.: 6429 Cov.: 32 AF XY: 0.283 AC XY: 21040 AN XY: 74408

African (AFR) AF: 0.324 AC: 13461 AN: 41512

American (AMR) AF: 0.244 AC: 3730 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2054 AN: 5186

South Asian (SAS) AF: 0.317 AC: 1526 AN: 4818

European-Finnish (FIN) AF: 0.182 AC: 1929 AN: 10580

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19048 AN: 67998

Other (OTH) AF: 0.288 AC: 609 AN: 2114

Alfa AF: 0.286 Hom.: 22853

Bravo AF: 0.293

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.80
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs3130517; hg19: chr6-31190303;