11-26854633-T-C

Variant names:

• chr11-26854633-T-C
• rs2122455
• ENST00000738475.1:n.1377T>C

Variant summary

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

The ENST00000738475.1(ENSG00000296353):​n.1377T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,930 control chromosomes in the GnomAD database, including 14,653 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 0.43 (14653 hom., cov: 33)
• Consequence: ENSG00000296353 ENST00000738475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 2 publications found

Genes affected

ENSG00000296353 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738475.1. 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
	ENSG00000296353	ENST00000738475.1		n.1377T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64934 AN: 151814 Hom.: 14639 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.428 AC: 64994 AN: 151930 Hom.: 14653 Cov.: 33 AF XY: 0.423 AC XY: 31369 AN XY: 74242

African (AFR) AF: 0.551 AC: 22845 AN: 41478

American (AMR) AF: 0.334 AC: 5087 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1153 AN: 5158

South Asian (SAS) AF: 0.413 AC: 1994 AN: 4826

European-Finnish (FIN) AF: 0.369 AC: 3905 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 139 AN: 286

European-Non Finnish (NFE) AF: 0.398 AC: 27035 AN: 67874

Other (OTH) AF: 0.425 AC: 896 AN: 2108

Alfa AF: 0.383 Hom.: 5330

Bravo AF: 0.426

Asia WGS AF: 0.355 AC: 1228 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.3
DANN	Benign	0.76
PhyloP100		0.0090

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: rs2122455;

hg19: chr11-26876180;