rs7739434

Positions:

• chr6-29962842-G-A

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 0.779 in 151,854 control chromosomes in the GnomAD database, including 46,616 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 0.78 (46616 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.779 AC: 118165 AN: 151738 Hom.: 46590 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.779 AC: 118226 AN: 151854 Hom.: 46616 Cov.: 31 AF XY: 0.782 AC XY: 58044 AN XY: 74222

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.764

Alfa AF: 0.817 Hom.: 37120

Bravo AF: 0.768

Asia WGS AF: 0.824 AC: 2846 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7739434; hg19: chr6-29930619;