6-29520472-A-G

Position:

• chr6-29520472-A-G

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 0.517 in 151,712 control chromosomes in the GnomAD database, including 20,702 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 0.52 (20702 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 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: 0.517 AC: 78406 AN: 151594 Hom.: 20672 Cov.: 30

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.517 AC: 78483 AN: 151712 Hom.: 20702 Cov.: 30 AF XY: 0.510 AC XY: 37849 AN XY: 74168

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.495

Alfa AF: 0.496 Hom.: 25317

Bravo AF: 0.528

Asia WGS AF: 0.386 AC: 1342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2745400; hg19: chr6-29488249; COSMIC: COSV61754501;