11-92946612-C-T

Variant names:

• chr11-92946612-C-T
• rs11523890
• ENST00000532770.2:n.147-13613C>T

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.147-13613C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,930 control chromosomes in the GnomAD database, including 10,550 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 0.37 (10550 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 10 publications found

Genes affected

ENSG00000254874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532770.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254874	ENST00000532770.2	TSL:2	n.147-13613C>T		intron	N/A
	ENSG00000254874	ENST00000749785.1		n.129-13613C>T		intron	N/A
	ENSG00000254874	ENST00000749786.1		n.116-13613C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56094 AN: 151812 Hom.: 10546 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.370 AC: 56140 AN: 151930 Hom.: 10550 Cov.: 32 AF XY: 0.370 AC XY: 27482 AN XY: 74232

African (AFR) AF: 0.424 AC: 17558 AN: 41416

American (AMR) AF: 0.287 AC: 4381 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3472

East Asian (EAS) AF: 0.444 AC: 2284 AN: 5148

South Asian (SAS) AF: 0.399 AC: 1917 AN: 4806

European-Finnish (FIN) AF: 0.399 AC: 4213 AN: 10558

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23355 AN: 67946

Other (OTH) AF: 0.373 AC: 786 AN: 2108

Alfa AF: 0.350 Hom.: 1309

Bravo AF: 0.361

Asia WGS AF: 0.364 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11523890;

hg19: chr11-92679778;