6-32699342-T-C

Variant names:

• chr6-32699342-T-C
• rs3135006

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 0.763 in 152,068 control chromosomes in the GnomAD database, including 44,506 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 0.76 (44506 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 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: 0.763 AC: 115962 AN: 151950 Hom.: 44475 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.763 AC: 116052 AN: 152068 Hom.: 44506 Cov.: 31 AF XY: 0.765 AC XY: 56882 AN XY: 74346

African (AFR) AF: 0.720 AC: 29871 AN: 41466

American (AMR) AF: 0.814 AC: 12448 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2925 AN: 3470

East Asian (EAS) AF: 0.906 AC: 4689 AN: 5178

South Asian (SAS) AF: 0.881 AC: 4250 AN: 4822

European-Finnish (FIN) AF: 0.753 AC: 7950 AN: 10552

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51211 AN: 67972

Other (OTH) AF: 0.799 AC: 1685 AN: 2108

Alfa AF: 0.760 Hom.: 124379

Bravo AF: 0.767

Asia WGS AF: 0.886 AC: 3081 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.38
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs3135006; hg19: chr6-32667119;