rs2034521

Variant names:

• chr15-42123072-C-A
• rs2034521

Your query was ambiguous. Multiple possible variants found:

• chr15-42123072-C-A
• chr15-42123072-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 0.323 in 152,074 control chromosomes in the GnomAD database, including 8,927 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 0.32 (8927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.323 AC: 49143 AN: 151956 Hom.: 8916 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.323 AC: 49169 AN: 152074 Hom.: 8927 Cov.: 32 AF XY: 0.328 AC XY: 24345 AN XY: 74308

African (AFR) AF: 0.182 AC: 7550 AN: 41502

American (AMR) AF: 0.465 AC: 7103 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3144 AN: 5156

South Asian (SAS) AF: 0.435 AC: 2094 AN: 4812

European-Finnish (FIN) AF: 0.297 AC: 3131 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23938 AN: 67978

Other (OTH) AF: 0.350 AC: 740 AN: 2112

Alfa AF: 0.344 Hom.: 27253

Bravo AF: 0.330

Asia WGS AF: 0.485 AC: 1686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.83
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2034521; hg19: chr15-42415270;