rs7696139

chr4-3774521-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;