chr6-29721109-C-A

Variant names:

• chr6-29721109-C-A
• rs1632447

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 0.826 in 151,852 control chromosomes in the GnomAD database, including 52,073 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 0.83 (52073 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.826 AC: 125336 AN: 151734 Hom.: 52013 Cov.: 30

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.826 AC: 125455 AN: 151852 Hom.: 52073 Cov.: 30 AF XY: 0.824 AC XY: 61117 AN XY: 74184

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.833

Alfa AF: 0.822 Hom.: 6402

Bravo AF: 0.838

Asia WGS AF: 0.941 AC: 3272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1632447; hg19: chr6-29688886;