rs4795408

chr17-39951374-G-A

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 0.416 in 151,856 control chromosomes in the GnomAD database, including 13,505 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 0.42 (13505 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.416 AC: 63179 AN: 151738 Hom.: 13511 Cov.: 30

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.416 AC: 63173 AN: 151856 Hom.: 13505 Cov.: 30 AF XY: 0.414 AC XY: 30710 AN XY: 74228

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.414

Alfa AF: 0.434 Hom.: 1800

Bravo AF: 0.426

Asia WGS AF: 0.457 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.2
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4795408; hg19: chr17-38107627;