chr6-32411606-G-C

Variant names:

• chr6-32411606-G-C
• rs3129962

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 0.206 in 151,970 control chromosomes in the GnomAD database, including 3,399 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 0.21 (3399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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: 0.206 AC: 31214 AN: 151854 Hom.: 3396 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.206 AC: 31230 AN: 151970 Hom.: 3399 Cov.: 32 AF XY: 0.211 AC XY: 15656 AN XY: 74260

African (AFR) AF: 0.209 AC: 8642 AN: 41404

American (AMR) AF: 0.187 AC: 2859 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.201 AC: 1035 AN: 5156

South Asian (SAS) AF: 0.155 AC: 747 AN: 4820

European-Finnish (FIN) AF: 0.326 AC: 3433 AN: 10544

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13307 AN: 67978

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.0180 Hom.: 238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs3129962; hg19: chr6-32379383;