6-163609768-A-G

Variant names:

• chr6-163609768-A-G
• rs6941513

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 0.449 in 151,932 control chromosomes in the GnomAD database, including 15,834 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 0.45 (15834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 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: 0.449 AC: 68102 AN: 151814 Hom.: 15805 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.449 AC: 68174 AN: 151932 Hom.: 15834 Cov.: 32 AF XY: 0.456 AC XY: 33856 AN XY: 74260

African (AFR) AF: 0.510 AC: 21124 AN: 41442

American (AMR) AF: 0.475 AC: 7253 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3468

East Asian (EAS) AF: 0.701 AC: 3615 AN: 5154

South Asian (SAS) AF: 0.551 AC: 2652 AN: 4814

European-Finnish (FIN) AF: 0.436 AC: 4589 AN: 10534

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26275 AN: 67938

Other (OTH) AF: 0.443 AC: 931 AN: 2102

Alfa AF: 0.416 Hom.: 1635

Bravo AF: 0.452

Asia WGS AF: 0.627 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6941513; hg19: chr6-164030800;