chr6-29913048-T-C

Variant names:

• chr6-29913048-T-C
• rs1611442

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 0.827 in 145,924 control chromosomes in the GnomAD database, including 52,269 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 (52269 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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: 0.827 AC: 120551 AN: 145814 Hom.: 52216 Cov.: 28

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.827 AC: 120660 AN: 145924 Hom.: 52269 Cov.: 28 AF XY: 0.823 AC XY: 58422 AN XY: 71020

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.847

Alfa AF: 0.812 Hom.: 5376

Asia WGS AF: 0.928 AC: 2888 AN: 3112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611442; hg19: chr6-29880825;