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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902649	XR_007062628.1	n.1445T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC124902649	XR_007062629.1	n.1668T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296353	ENST00000738475.1	n.1377T>C		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs2122455; hg19: chr11-26876180;