rs11666981

Variant names:

• chr19-22542766-C-T
• rs11666981

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 0.177 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0721 AC: 2996 AN: 41534

American (AMR) AF: 0.238 AC: 3636 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3470

East Asian (EAS) AF: 0.132 AC: 681 AN: 5150

South Asian (SAS) AF: 0.186 AC: 894 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2150 AN: 10588

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15088 AN: 67964

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.191 Hom.: 396

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11666981; hg19: chr19-22725568;