chr11-92940662-C-T

Variant names:

• chr11-92940662-C-T
• rs1387153
• ENST00000532770.2:n.146+9656C>T

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.146+9656C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,984 control chromosomes in the GnomAD database, including 7,801 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 0.32 (7801 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 232 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=-0.98).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254874	ENST00000532770.2	TSL:2	n.146+9656C>T		intron	N/A
	ENSG00000254874	ENST00000749785.1		n.128+9656C>T		intron	N/A
	ENSG00000254874	ENST00000749786.1		n.115+9656C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48157 AN: 151864 Hom.: 7801 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.317 AC: 48184 AN: 151984 Hom.: 7801 Cov.: 32 AF XY: 0.319 AC XY: 23711 AN XY: 74272

African (AFR) AF: 0.356 AC: 14774 AN: 41458

American (AMR) AF: 0.235 AC: 3589 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 961 AN: 3462

East Asian (EAS) AF: 0.444 AC: 2289 AN: 5154

South Asian (SAS) AF: 0.390 AC: 1875 AN: 4804

European-Finnish (FIN) AF: 0.354 AC: 3738 AN: 10548

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19781 AN: 67962

Other (OTH) AF: 0.301 AC: 635 AN: 2112

Alfa AF: 0.295 Hom.: 32121

Bravo AF: 0.308

Asia WGS AF: 0.354 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.54
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs1387153; hg19: chr11-92673828;