6-29952759-G-T

Position:

• chr6-29952759-G-T

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 0.65 in 151,372 control chromosomes in the GnomAD database, including 32,287 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 0.65 (32287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98309 AN: 151254 Hom.: 32230 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.650 AC: 98417 AN: 151372 Hom.: 32287 Cov.: 32 AF XY: 0.650 AC XY: 48052 AN XY: 73952

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.664

Alfa AF: 0.561 Hom.: 2206

Bravo AF: 0.665

Asia WGS AF: 0.704 AC: 2426 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2975042; hg19: chr6-29920536;