rs4795397

Variant names:

• chr17-39867492-A-G
• rs4795397

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 0.384 in 151,136 control chromosomes in the GnomAD database, including 12,104 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 0.38 (12104 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 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: 0.384 AC: 58006 AN: 151016 Hom.: 12091 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.368

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.384 AC: 58045 AN: 151136 Hom.: 12104 Cov.: 31 AF XY: 0.387 AC XY: 28624 AN XY: 73906

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.373

Alfa AF: 0.373 Hom.: 1995

Bravo AF: 0.357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4795397; hg19: chr17-38023745;