6-41411577-G-A

Variant names:

• chr6-41411577-G-A
• rs7762544

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 0.812 in 152,138 control chromosomes in the GnomAD database, including 50,349 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 0.81 (50349 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.812 AC: 123427 AN: 152020 Hom.: 50299 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.812 AC: 123537 AN: 152138 Hom.: 50349 Cov.: 31 AF XY: 0.815 AC XY: 60586 AN XY: 74360

African (AFR) AF: 0.784 AC: 32527 AN: 41472

American (AMR) AF: 0.824 AC: 12602 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2517 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5158 AN: 5184

South Asian (SAS) AF: 0.862 AC: 4157 AN: 4820

European-Finnish (FIN) AF: 0.859 AC: 9104 AN: 10602

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55048 AN: 67982

Other (OTH) AF: 0.771 AC: 1626 AN: 2108

Alfa AF: 0.807 Hom.: 25585

Bravo AF: 0.807

Asia WGS AF: 0.911 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.66
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7762544; hg19: chr6-41379315;