rs4795397

chr17-39867492-A-G

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/exons	MANE	UniProt

Ensembl

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