19-47898636-G-A

Variant names:

• chr19-47898636-G-A
• rs2637125

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 0.111 in 151,964 control chromosomes in the GnomAD database, including 1,279 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 0.11 (1279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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: 0.111 AC: 16881 AN: 151846 Hom.: 1281 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.111 AC: 16876 AN: 151964 Hom.: 1279 Cov.: 32 AF XY: 0.112 AC XY: 8301 AN XY: 74292

African (AFR) AF: 0.0270 AC: 1118 AN: 41462

American (AMR) AF: 0.0842 AC: 1285 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3468

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5172

South Asian (SAS) AF: 0.124 AC: 596 AN: 4808

European-Finnish (FIN) AF: 0.197 AC: 2076 AN: 10546

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10630 AN: 67930

Other (OTH) AF: 0.111 AC: 234 AN: 2112

Alfa AF: 0.127 Hom.: 609

Bravo AF: 0.0993

Asia WGS AF: 0.0530 AC: 185 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	1.3
DANN	Benign	0.67
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2637125; hg19: chr19-48401893;