chr17-39951374-G-A

Variant names:

• chr17-39951374-G-A
• rs4795408

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.321 AC: 13270 AN: 41388

American (AMR) AF: 0.467 AC: 7127 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3464

East Asian (EAS) AF: 0.551 AC: 2832 AN: 5142

South Asian (SAS) AF: 0.449 AC: 2160 AN: 4810

European-Finnish (FIN) AF: 0.375 AC: 3959 AN: 10554

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30928 AN: 67924

Other (OTH) AF: 0.414 AC: 871 AN: 2106

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
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs4795408; hg19: chr17-38107627;