rs1916792

Variant names:

• chr11-114855290-T-A
• rs1916792
• ENST00000751459.1:n.192+17391A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751459.1(ENSG00000297869):​n.192+17391A>T variant causes a intron 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: ENSG00000297869 ENST00000751459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 2 publications found

Genes affected

ENSG00000297869 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751459.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297869	ENST00000751459.1		n.192+17391A>T		intron	N/A
	ENSG00000297869	ENST00000751460.1		n.214+17391A>T		intron	N/A

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

African (AFR) AF: 0.305 AC: 12652 AN: 41488

American (AMR) AF: 0.435 AC: 6649 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2547 AN: 5160

South Asian (SAS) AF: 0.482 AC: 2322 AN: 4822

European-Finnish (FIN) AF: 0.559 AC: 5904 AN: 10556

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38941 AN: 67976

Other (OTH) AF: 0.512 AC: 1081 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.61
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs1916792; hg19: chr11-114726012;