6-140979939-A-G

Variant names:

• chr6-140979939-A-G
• rs1856363

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 0.683 in 151,840 control chromosomes in the GnomAD database, including 35,968 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 0.68 (35968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103683 AN: 151722 Hom.: 35943 Cov.: 31

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.683 AC: 103744 AN: 151840 Hom.: 35968 Cov.: 31 AF XY: 0.674 AC XY: 50020 AN XY: 74194

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.688

Alfa AF: 0.675 Hom.: 15811

Bravo AF: 0.687

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1856363; hg19: chr6-141301076; COSMIC: COSV60288788;