rs3109881

Variant names:

• chr15-50547075-G-A
• rs3109881

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 0.354 in 151,652 control chromosomes in the GnomAD database, including 10,582 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 0.35 (10582 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.475 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: 0.354 AC: 53696 AN: 151536 Hom.: 10582 Cov.: 30

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.354 AC: 53708 AN: 151652 Hom.: 10582 Cov.: 30 AF XY: 0.360 AC XY: 26670 AN XY: 74060

African (AFR) AF: 0.176 AC: 7263 AN: 41316

American (AMR) AF: 0.484 AC: 7369 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2411 AN: 5152

South Asian (SAS) AF: 0.388 AC: 1860 AN: 4798

European-Finnish (FIN) AF: 0.408 AC: 4278 AN: 10496

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27740 AN: 67894

Other (OTH) AF: 0.406 AC: 856 AN: 2106

Alfa AF: 0.358 Hom.: 1354

Bravo AF: 0.355

Asia WGS AF: 0.354 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.9
DANN	Benign	0.79
PhyloP100		1.3
PromoterAI		0.0036	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3109881; hg19: chr15-50839272;