rs905739

Variant names:

• chr15-78552768-A-G
• rs905739

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 0.273 in 152,124 control chromosomes in the GnomAD database, including 6,387 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 0.27 (6387 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 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: 0.272 AC: 41420 AN: 152006 Hom.: 6370 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.273 AC: 41458 AN: 152124 Hom.: 6387 Cov.: 33 AF XY: 0.281 AC XY: 20879 AN XY: 74378

African (AFR) AF: 0.254 AC: 10519 AN: 41468

American (AMR) AF: 0.478 AC: 7305 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2244 AN: 5178

South Asian (SAS) AF: 0.404 AC: 1952 AN: 4828

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10574

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14848 AN: 68008

Other (OTH) AF: 0.287 AC: 606 AN: 2114

Alfa AF: 0.240 Hom.: 990

Bravo AF: 0.286

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.39
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs905739; hg19: chr15-78845110;