rs11669754

Variant names:

• chr19-53194115-T-G
• rs11669754

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 0.35 in 149,668 control chromosomes in the GnomAD database, including 9,736 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 0.35 (9736 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 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: 0.350 AC: 52302 AN: 149552 Hom.: 9728 Cov.: 27

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.350 AC: 52335 AN: 149668 Hom.: 9736 Cov.: 27 AF XY: 0.341 AC XY: 24887 AN XY: 73030

African (AFR) AF: 0.422 AC: 17007 AN: 40340

American (AMR) AF: 0.289 AC: 4331 AN: 14988

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1755 AN: 3438

East Asian (EAS) AF: 0.0280 AC: 144 AN: 5150

South Asian (SAS) AF: 0.179 AC: 854 AN: 4780

European-Finnish (FIN) AF: 0.320 AC: 3259 AN: 10190

Middle Eastern (MID) AF: 0.486 AC: 141 AN: 290

European-Non Finnish (NFE) AF: 0.352 AC: 23800 AN: 67532

Other (OTH) AF: 0.358 AC: 736 AN: 2058

Alfa AF: 0.349 Hom.: 7256

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11669754; hg19: chr19-53697368;