6-113930971-A-G

Variant names:

• chr6-113930971-A-G
• rs13212283

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 0.405 in 151,850 control chromosomes in the GnomAD database, including 13,211 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 0.41 (13211 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61473 AN: 151732 Hom.: 13195 Cov.: 30

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.405 AC: 61507 AN: 151850 Hom.: 13211 Cov.: 30 AF XY: 0.406 AC XY: 30132 AN XY: 74204

African (AFR) AF: 0.264 AC: 10948 AN: 41436

American (AMR) AF: 0.394 AC: 6015 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3464

East Asian (EAS) AF: 0.657 AC: 3368 AN: 5128

South Asian (SAS) AF: 0.500 AC: 2407 AN: 4814

European-Finnish (FIN) AF: 0.421 AC: 4433 AN: 10532

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31194 AN: 67902

Other (OTH) AF: 0.431 AC: 909 AN: 2108

Alfa AF: 0.376 Hom.: 2499

Bravo AF: 0.398

Asia WGS AF: 0.588 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs13212283; hg19: chr6-114252135;