chr19-19144116-C-T

Variant names:

• chr19-19144116-C-T
• rs11669988

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 0.122 in 148,984 control chromosomes in the GnomAD database, including 1,336 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 0.12 (1336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.122 AC: 18149 AN: 148856 Hom.: 1333 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0224

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.122 AC: 18165 AN: 148984 Hom.: 1336 Cov.: 31 AF XY: 0.125 AC XY: 9102 AN XY: 72748

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.0809

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.107

Alfa AF: 0.103 Hom.: 1492

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11669988; hg19: chr19-19254925;