6-32773229-T-C

Variant names:

• chr6-32773229-T-C
• rs2621419

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 0.698 in 151,996 control chromosomes in the GnomAD database, including 37,090 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 0.70 (37090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 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: 0.698 AC: 105990 AN: 151878 Hom.: 37075 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.698 AC: 106050 AN: 151996 Hom.: 37090 Cov.: 32 AF XY: 0.703 AC XY: 52198 AN XY: 74296

African (AFR) AF: 0.666 AC: 27615 AN: 41444

American (AMR) AF: 0.694 AC: 10605 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2484 AN: 3470

East Asian (EAS) AF: 0.733 AC: 3786 AN: 5166

South Asian (SAS) AF: 0.736 AC: 3548 AN: 4820

European-Finnish (FIN) AF: 0.791 AC: 8356 AN: 10564

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47249 AN: 67928

Other (OTH) AF: 0.698 AC: 1473 AN: 2110

Alfa AF: 0.696 Hom.: 21558

Bravo AF: 0.687

Asia WGS AF: 0.753 AC: 2617 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs2621419; hg19: chr6-32741006;