rs732841

Variant names:

• chr19-45704552-A-C
• rs732841

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 0.0669 in 152,140 control chromosomes in the GnomAD database, including 457 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 0.067 (457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0669 AC: 10174 AN: 152022 Hom.: 455 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0669 AC: 10179 AN: 152140 Hom.: 457 Cov.: 32 AF XY: 0.0654 AC XY: 4864 AN XY: 74362

African (AFR) AF: 0.120 AC: 4975 AN: 41492

American (AMR) AF: 0.0337 AC: 514 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 310 AN: 3468

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5184

South Asian (SAS) AF: 0.0975 AC: 469 AN: 4810

European-Finnish (FIN) AF: 0.0385 AC: 409 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0490 AC: 3333 AN: 67994

Other (OTH) AF: 0.0579 AC: 122 AN: 2108

Alfa AF: 0.0528 Hom.: 446

Bravo AF: 0.0665

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.36
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs732841; hg19: chr19-46207810;