rs11666694

chr19-2953811-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 0.252 in 152,042 control chromosomes in the GnomAD database, including 6,106 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 0.25 (6106 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.252 AC: 38305 AN: 151924 Hom.: 6110 Cov.: 31

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.252 AC: 38287 AN: 152042 Hom.: 6106 Cov.: 31 AF XY: 0.252 AC XY: 18749 AN XY: 74320

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.268

Alfa AF: 0.314 Hom.: 4430

Bravo AF: 0.234

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.7
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11666694; hg19: chr19-2953809; COSMIC: COSV53435600;