6-32420769-T-C

Variant names:

• chr6-32420769-T-C
• rs2213581

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 0.805 in 152,186 control chromosomes in the GnomAD database, including 49,537 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 0.80 (49537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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: 0.805 AC: 122364 AN: 152068 Hom.: 49505 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.805 AC: 122448 AN: 152186 Hom.: 49537 Cov.: 32 AF XY: 0.810 AC XY: 60282 AN XY: 74406

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.812

Alfa AF: 0.795 Hom.: 15236

Bravo AF: 0.797

Asia WGS AF: 0.922 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
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: rs2213581; hg19: chr6-32388546;