6-141173541-A-G

Variant names:

• chr6-141173541-A-G
• rs1349710

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 0.72 in 152,038 control chromosomes in the GnomAD database, including 39,752 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 0.72 (39752 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 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: 0.719 AC: 109286 AN: 151920 Hom.: 39706 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.720 AC: 109394 AN: 152038 Hom.: 39752 Cov.: 31 AF XY: 0.719 AC XY: 53409 AN XY: 74314

African (AFR) AF: 0.791 AC: 32808 AN: 41468

American (AMR) AF: 0.735 AC: 11232 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4592 AN: 5160

South Asian (SAS) AF: 0.746 AC: 3591 AN: 4816

European-Finnish (FIN) AF: 0.634 AC: 6691 AN: 10552

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45726 AN: 67972

Other (OTH) AF: 0.740 AC: 1562 AN: 2110

Alfa AF: 0.718 Hom.: 6864

Bravo AF: 0.732

Asia WGS AF: 0.811 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.50
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1349710; hg19: chr6-141494678;