rs7739434

Variant names:

• chr6-29962842-G-A
• rs7739434

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;