rs7696139

Variant names:

• chr4-3774521-G-C
• rs7696139

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 0.657 in 152,134 control chromosomes in the GnomAD database, including 34,415 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 0.66 (34415 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 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: 0.657 AC: 99948 AN: 152016 Hom.: 34401 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.657 AC: 99995 AN: 152134 Hom.: 34415 Cov.: 33 AF XY: 0.658 AC XY: 48919 AN XY: 74390

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.704

Alfa AF: 0.707 Hom.: 4881

Bravo AF: 0.629

Asia WGS AF: 0.651 AC: 2262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7696139; hg19: chr4-3776248;