6-32710069-T-C

Position:

• chr6-32710069-T-C

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 0.687 in 151,252 control chromosomes in the GnomAD database, including 35,998 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 0.69 (35998 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 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: 0.687 AC: 103781 AN: 151132 Hom.: 35987 Cov.: 28

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.687 AC: 103852 AN: 151252 Hom.: 35998 Cov.: 28 AF XY: 0.685 AC XY: 50596 AN XY: 73894

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.732

Alfa AF: 0.690 Hom.: 18381

Bravo AF: 0.692

Asia WGS AF: 0.772 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4947344; hg19: chr6-32677846; COSMIC: COSV70582399;