rs2113103

Variant names:

• chr19-41022762-G-A
• rs2113103

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.140 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

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.141

Alfa AF: 0.137 Hom.: 276

Bravo AF: 0.134

Asia WGS AF: 0.191 AC: 665 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	4.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2113103; hg19: chr19-41528667;