rs576556

Variant names:

• chr19-33843952-G-A
• rs576556

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 0.356 in 151,260 control chromosomes in the GnomAD database, including 9,687 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 0.36 (9687 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 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: 0.356 AC: 53877 AN: 151142 Hom.: 9682 Cov.: 28

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.356 AC: 53912 AN: 151260 Hom.: 9687 Cov.: 28 AF XY: 0.357 AC XY: 26381 AN XY: 73862

African (AFR) AF: 0.385 AC: 15872 AN: 41176

American (AMR) AF: 0.368 AC: 5586 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3468

East Asian (EAS) AF: 0.144 AC: 739 AN: 5140

South Asian (SAS) AF: 0.301 AC: 1443 AN: 4790

European-Finnish (FIN) AF: 0.407 AC: 4210 AN: 10348

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23795 AN: 67856

Other (OTH) AF: 0.330 AC: 691 AN: 2092

Alfa AF: 0.354 Hom.: 7981

Bravo AF: 0.359

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.37
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs576556; hg19: chr19-34334857;