rs7635839

Variant names:

• chr3-191949988-G-A
• rs7635839

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 0.0605 in 152,210 control chromosomes in the GnomAD database, including 697 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 0.061 (697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 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: 0.0604 AC: 9189 AN: 152092 Hom.: 694 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0224

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0605 AC: 9215 AN: 152210 Hom.: 697 Cov.: 32 AF XY: 0.0588 AC XY: 4378 AN XY: 74440

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.0195

Gnomad4 FIN AF: 0.00603

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0197 Hom.: 261

Bravo AF: 0.0685

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7635839; hg19: chr3-191667777;