chr19-52098146-G-A

Variant names:

• chr19-52098146-G-A
• rs11666341

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 0.181 in 152,076 control chromosomes in the GnomAD database, including 2,947 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 0.18 (2947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 20 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 (EAS) allele frequency at 95% confidence interval = 0.459 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: 0.181 AC: 27571 AN: 151958 Hom.: 2942 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.181 AC: 27600 AN: 152076 Hom.: 2947 Cov.: 32 AF XY: 0.185 AC XY: 13776 AN XY: 74342

African (AFR) AF: 0.126 AC: 5210 AN: 41504

American (AMR) AF: 0.200 AC: 3061 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 425 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2447 AN: 5152

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4816

European-Finnish (FIN) AF: 0.171 AC: 1801 AN: 10560

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12683 AN: 67980

Other (OTH) AF: 0.186 AC: 392 AN: 2108

Alfa AF: 0.187 Hom.: 8503

Bravo AF: 0.180

Asia WGS AF: 0.368 AC: 1277 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	9.2
DANN	Benign	0.60
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11666341; hg19: chr19-52601399;