6-32608701-T-C

Position:

• chr6-32608701-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 0.745 in 150,784 control chromosomes in the GnomAD database, including 42,077 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 0.74 (42077 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.745 AC: 112188 AN: 150662 Hom.: 42042 Cov.: 29

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.745 AC: 112276 AN: 150784 Hom.: 42077 Cov.: 29 AF XY: 0.742 AC XY: 54666 AN XY: 73696

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.771

Alfa AF: 0.735 Hom.: 36080

Bravo AF: 0.759

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271100; hg19: chr6-32576478;