6-81032568-G-T

Variant names:

• chr6-81032568-G-T
• rs724993

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 0.121 in 151,958 control chromosomes in the GnomAD database, including 1,206 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 0.12 (1206 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.16 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: 0.121 AC: 18380 AN: 151840 Hom.: 1206 Cov.: 32

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.121 AC: 18385 AN: 151958 Hom.: 1206 Cov.: 32 AF XY: 0.119 AC XY: 8865 AN XY: 74254

Gnomad4 AFR AF: 0.0773

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0890

Gnomad4 EAS AF: 0.0983

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0854

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0568 Hom.: 57

Bravo AF: 0.129

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs724993; hg19: chr6-81742285; COSMIC: COSV69408474;