6-32797405-G-A

Position:

• chr6-32797405-G-A

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 0.892 in 152,130 control chromosomes in the GnomAD database, including 60,572 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 0.89 (60572 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135566 AN: 152012 Hom.: 60519 Cov.: 30

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.892 AC: 135680 AN: 152130 Hom.: 60572 Cov.: 30 AF XY: 0.894 AC XY: 66483 AN XY: 74392

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.975

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.907

Alfa AF: 0.875 Hom.: 36644

Bravo AF: 0.894

Asia WGS AF: 0.936 AC: 3255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7767167; hg19: chr6-32765182;