19-41022762-G-A

Variant names:

• chr19-41022762-G-A
• rs2113103

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 0.14 in 152,150 control chromosomes in the GnomAD database, including 1,645 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 0.14 (1645 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.916
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21314 AN: 152032 Hom.: 1639 Cov.: 31

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.140 AC: 21349 AN: 152150 Hom.: 1645 Cov.: 31 AF XY: 0.142 AC XY: 10562 AN XY: 74368

African (AFR) AF: 0.100 AC: 4164 AN: 41534

American (AMR) AF: 0.107 AC: 1641 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1386 AN: 5162

South Asian (SAS) AF: 0.167 AC: 802 AN: 4812

European-Finnish (FIN) AF: 0.172 AC: 1817 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10757 AN: 67980

Other (OTH) AF: 0.141 AC: 298 AN: 2112

Alfa AF: 0.133 Hom.: 493

Bravo AF: 0.134

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.69
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs2113103; hg19: chr19-41528667;