rs2113103

Positions:

• chr19-41022762-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;