chr6-141281542-A-G

Position:

• chr6-141281542-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 0.0828 in 152,166 control chromosomes in the GnomAD database, including 804 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 0.083 (804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0827 AC: 12569 AN: 152048 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0828 AC: 12595 AN: 152166 Hom.: 804 Cov.: 32 AF XY: 0.0849 AC XY: 6319 AN XY: 74390

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0490 Hom.: 336

Bravo AF: 0.0842

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321807; hg19: chr6-141602679;