6-29520472-A-G

Variant names:

• chr6-29520472-A-G
• rs2745400

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;