rs11669754

chr19-53194115-T-G

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 0.35 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.0280

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.358

Alfa AF: 0.354 Hom.: 5200

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11669754; hg19: chr19-53697368;