chr6-141173541-A-G

Position:

• chr6-141173541-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.740

Alfa AF: 0.716 Hom.: 6630

Bravo AF: 0.732

Asia WGS AF: 0.811 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349710; hg19: chr6-141494678;