rs2546057

Positions:

• chr19-33829949-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.418

Alfa AF: 0.451 Hom.: 2607

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2546057; hg19: chr19-34320854;