rs11669988

Variant names:

• chr19-19144116-C-T
• rs11669988

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 0.122 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.135 AC: 5476 AN: 40422

American (AMR) AF: 0.115 AC: 1718 AN: 14896

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 454 AN: 3440

East Asian (EAS) AF: 0.337 AC: 1674 AN: 4974

South Asian (SAS) AF: 0.281 AC: 1325 AN: 4718

European-Finnish (FIN) AF: 0.0809 AC: 821 AN: 10148

Middle Eastern (MID) AF: 0.161 AC: 40 AN: 248

European-Non Finnish (NFE) AF: 0.0955 AC: 6413 AN: 67160

Other (OTH) AF: 0.107 AC: 224 AN: 2086

Alfa AF: 0.106 Hom.: 3589

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11669988; hg19: chr19-19254925;