6-41287773-A-G

Variant names:

• chr6-41287773-A-G
• rs7768162

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 0.739 in 152,038 control chromosomes in the GnomAD database, including 42,333 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 0.74 (42333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 12 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 = 0.882 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112325 AN: 151920 Hom.: 42283 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.739 AC: 112429 AN: 152038 Hom.: 42333 Cov.: 32 AF XY: 0.734 AC XY: 54584 AN XY: 74316

African (AFR) AF: 0.890 AC: 36914 AN: 41486

American (AMR) AF: 0.755 AC: 11530 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2319 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2955 AN: 5176

South Asian (SAS) AF: 0.561 AC: 2704 AN: 4816

European-Finnish (FIN) AF: 0.637 AC: 6707 AN: 10532

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46850 AN: 67966

Other (OTH) AF: 0.748 AC: 1579 AN: 2110

Alfa AF: 0.703 Hom.: 16972

Bravo AF: 0.759

Asia WGS AF: 0.557 AC: 1928 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.61
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs7768162; hg19: chr6-41255511;