rs4803953

Variant names:

• chr19-46455750-C-A
• rs4803953

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 0.162 in 151,532 control chromosomes in the GnomAD database, including 2,300 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 0.16 (2300 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 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: 0.162 AC: 24578 AN: 151414 Hom.: 2297 Cov.: 29

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.162 AC: 24602 AN: 151532 Hom.: 2300 Cov.: 29 AF XY: 0.156 AC XY: 11554 AN XY: 74056

African (AFR) AF: 0.215 AC: 8806 AN: 41040

American (AMR) AF: 0.135 AC: 2060 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3468

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5172

South Asian (SAS) AF: 0.0411 AC: 198 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1352 AN: 10528

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11228 AN: 67954

Other (OTH) AF: 0.158 AC: 333 AN: 2110

Alfa AF: 0.157 Hom.: 7860

Bravo AF: 0.166

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4803953; hg19: chr19-46959007;