6-31513749-G-T

Variant names:

• chr6-31513749-G-T
• rs2516398

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 0.699 in 151,798 control chromosomes in the GnomAD database, including 37,236 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 0.70 (37236 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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: 0.699 AC: 106024 AN: 151680 Hom.: 37204 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.699 AC: 106104 AN: 151798 Hom.: 37236 Cov.: 31 AF XY: 0.702 AC XY: 52087 AN XY: 74204

African (AFR) AF: 0.738 AC: 30558 AN: 41392

American (AMR) AF: 0.636 AC: 9705 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2850 AN: 3468

East Asian (EAS) AF: 0.738 AC: 3803 AN: 5152

South Asian (SAS) AF: 0.726 AC: 3500 AN: 4818

European-Finnish (FIN) AF: 0.763 AC: 8040 AN: 10540

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.668 AC: 45356 AN: 67872

Other (OTH) AF: 0.696 AC: 1468 AN: 2110

Alfa AF: 0.688 Hom.: 59765

Bravo AF: 0.690

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.73
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2516398; hg19: chr6-31481526;