ENST00000813938.1:n.518+3150T>C

Variant names:

• chr11-119824741-T-C
• rs525914
• ENST00000813938.1:n.518+3150T>C

Variant summary

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

The ENST00000813938.1(ENSG00000287545):​n.518+3150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,158 control chromosomes in the GnomAD database, including 47,514 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 0.79 (47514 hom., cov: 33)
• Consequence: ENSG00000287545 ENST00000813938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 3 publications found

Genes affected

ENSG00000287545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813938.1. 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
	ENSG00000287545	ENST00000813938.1		n.518+3150T>C		intron	N/A
	ENSG00000287545	ENST00000813939.1		n.309+3150T>C		intron	N/A
	ENSG00000287545	ENST00000813940.1		n.268+3150T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119616 AN: 152040 Hom.: 47466 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.787 AC: 119721 AN: 152158 Hom.: 47514 Cov.: 33 AF XY: 0.791 AC XY: 58830 AN XY: 74400

African (AFR) AF: 0.688 AC: 28552 AN: 41494

American (AMR) AF: 0.857 AC: 13115 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2803 AN: 3466

East Asian (EAS) AF: 0.787 AC: 4059 AN: 5160

South Asian (SAS) AF: 0.739 AC: 3564 AN: 4824

European-Finnish (FIN) AF: 0.869 AC: 9221 AN: 10616

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55707 AN: 67978

Other (OTH) AF: 0.793 AC: 1675 AN: 2112

Alfa AF: 0.801 Hom.: 15802

Bravo AF: 0.781

Asia WGS AF: 0.761 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs525914; hg19: chr11-119695450; COSMIC: COSV73205669;