chr6-31526425-A-G

Variant names:

• chr6-31526425-A-G
• rs2516486

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 0.127 in 152,170 control chromosomes in the GnomAD database, including 1,453 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 0.13 (1453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 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: 0.127 AC: 19329 AN: 152052 Hom.: 1451 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.127 AC: 19350 AN: 152170 Hom.: 1453 Cov.: 32 AF XY: 0.135 AC XY: 10031 AN XY: 74390

African (AFR) AF: 0.0999 AC: 4148 AN: 41526

American (AMR) AF: 0.0912 AC: 1394 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1012 AN: 5162

South Asian (SAS) AF: 0.200 AC: 965 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2582 AN: 10588

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

European-Non Finnish (NFE) AF: 0.120 AC: 8193 AN: 68008

Other (OTH) AF: 0.129 AC: 272 AN: 2108

Alfa AF: 0.113 Hom.: 122

Bravo AF: 0.111

Asia WGS AF: 0.158 AC: 547 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	8.4
DANN	Benign	0.81
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs2516486; hg19: chr6-31494202;