rs2546057

Variant names:

• chr19-33829949-A-C
• rs2546057

Your query was ambiguous. Multiple possible variants found:

• chr19-33829949-A-C
• chr19-33829949-A-G
• chr19-33829949-A-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 0.411 in 152,002 control chromosomes in the GnomAD database, including 13,666 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 0.41 (13666 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 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: 0.411 AC: 62418 AN: 151884 Hom.: 13666 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.411 AC: 62433 AN: 152002 Hom.: 13666 Cov.: 32 AF XY: 0.412 AC XY: 30585 AN XY: 74296

African (AFR) AF: 0.275 AC: 11406 AN: 41452

American (AMR) AF: 0.500 AC: 7622 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.151 AC: 780 AN: 5182

South Asian (SAS) AF: 0.404 AC: 1949 AN: 4824

European-Finnish (FIN) AF: 0.487 AC: 5148 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32582 AN: 67946

Other (OTH) AF: 0.418 AC: 881 AN: 2106

Alfa AF: 0.401 Hom.: 5353

Bravo AF: 0.404

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.0
DANN	Benign	0.64
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2546057; hg19: chr19-34320854;