6-29911752-C-T

Variant names:

• chr6-29911752-C-T
• rs2524024

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 0.86 in 145,858 control chromosomes in the GnomAD database, including 55,927 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 0.86 (55927 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 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: 0.860 AC: 125384 AN: 145752 Hom.: 55870 Cov.: 28

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.897

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.860 AC: 125494 AN: 145858 Hom.: 55927 Cov.: 28 AF XY: 0.856 AC XY: 60834 AN XY: 71056

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.878

Alfa AF: 0.869 Hom.: 19637

Asia WGS AF: 0.947 AC: 2947 AN: 3112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524024; hg19: chr6-29879529;