rs1916792

chr11-114855290-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_948042.3(LOC105369506):n.86+17391A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,062 control chromosomes in the GnomAD database, including 18,422 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 0.48 (18422 hom., cov: 33)
• Consequence: LOC105369506 XR_948042.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

LOC105369506 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369506	XR_948042.3	n.86+17391A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72731 AN: 151944 Hom.: 18420 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.478 AC: 72759 AN: 152062 Hom.: 18422 Cov.: 33 AF XY: 0.473 AC XY: 35153 AN XY: 74312

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.512

Alfa AF: 0.519 Hom.: 2680

Bravo AF: 0.467

Asia WGS AF: 0.465 AC: 1616 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.5
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1916792; hg19: chr11-114726012;