rs2725544

Variant names:

• chr15-48700700-C-A
• rs2725544

Your query was ambiguous. Multiple possible variants found:

• chr15-48700700-C-A
• chr15-48700700-C-T

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 0.773 in 152,226 control chromosomes in the GnomAD database, including 45,703 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 0.77 (45703 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.773 AC: 117528 AN: 152108 Hom.: 45671 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.773 AC: 117612 AN: 152226 Hom.: 45703 Cov.: 33 AF XY: 0.780 AC XY: 58037 AN XY: 74428

African (AFR) AF: 0.707 AC: 29339 AN: 41514

American (AMR) AF: 0.805 AC: 12317 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2579 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5180 AN: 5188

South Asian (SAS) AF: 0.879 AC: 4239 AN: 4820

European-Finnish (FIN) AF: 0.862 AC: 9147 AN: 10612

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52243 AN: 68010

Other (OTH) AF: 0.780 AC: 1648 AN: 2112

Alfa AF: 0.771 Hom.: 38820

Bravo AF: 0.766

Asia WGS AF: 0.911 AC: 3168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.64
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs2725544; hg19: chr15-48992897;