chr6-81032568-G-T

Variant names:

• chr6-81032568-G-T
• rs724993

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 0.121 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0773 AC: 3197 AN: 41356

American (AMR) AF: 0.166 AC: 2524 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3472

East Asian (EAS) AF: 0.0983 AC: 508 AN: 5166

South Asian (SAS) AF: 0.116 AC: 559 AN: 4834

European-Finnish (FIN) AF: 0.0854 AC: 905 AN: 10596

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9967 AN: 67984

Other (OTH) AF: 0.129 AC: 271 AN: 2106

Alfa AF: 0.0576 Hom.: 62

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
PhyloP100		0.20

Splicing

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

Other links and lift over

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