rs3826041

Variant names:

• chr15-74726549-A-C
• rs3826041

Your query was ambiguous. Multiple possible variants found:

• chr15-74726549-A-C
• chr15-74726549-A-G

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 0.309 in 151,810 control chromosomes in the GnomAD database, including 9,647 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 0.31 (9647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.308 AC: 46792 AN: 151692 Hom.: 9602 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.309 AC: 46913 AN: 151810 Hom.: 9647 Cov.: 32 AF XY: 0.313 AC XY: 23218 AN XY: 74202

African (AFR) AF: 0.539 AC: 22354 AN: 41440

American (AMR) AF: 0.416 AC: 6350 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2660 AN: 5114

South Asian (SAS) AF: 0.353 AC: 1697 AN: 4806

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10564

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

European-Non Finnish (NFE) AF: 0.155 AC: 10501 AN: 67820

Other (OTH) AF: 0.301 AC: 636 AN: 2114

Alfa AF: 0.235 Hom.: 680

Bravo AF: 0.337

Asia WGS AF: 0.491 AC: 1702 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.58
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs3826041; hg19: chr15-75018890;