rs11666981

chr19-22542766-C-T

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 0.177 in 152,136 control chromosomes in the GnomAD database, including 2,837 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 0.18 (2837 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26927 AN: 152018 Hom.: 2834 Cov.: 30

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.177 AC: 26949 AN: 152136 Hom.: 2837 Cov.: 30 AF XY: 0.180 AC XY: 13379 AN XY: 74374

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.179

Alfa AF: 0.196 Hom.: 394

Bravo AF: 0.172

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.7
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: rs11666981; hg19: chr19-22725568;