11-127027082-C-T

Variant names:

• chr11-127027082-C-T
• rs503397
• ENST00000530177.2:n.154+5175C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000530177.2(ENSG00000255087):​n.154+5175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,108 control chromosomes in the GnomAD database, including 10,123 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 0.35 (10123 hom., cov: 33)
• Consequence: ENSG00000255087 ENST00000530177.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

ENSG00000255087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255087	ENST00000530177.2	n.154+5175C>T		intron_variant	Intron 1 of 7	4
ENSG00000255087	ENST00000647195.1	n.143+5175C>T		intron_variant	Intron 1 of 9
ENSG00000255087	ENST00000654157.1	n.150+5175C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53771 AN: 151990 Hom.: 10111 Cov.: 33

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.354 AC: 53830 AN: 152108 Hom.: 10123 Cov.: 33 AF XY: 0.360 AC XY: 26787 AN XY: 74354

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.324

Alfa AF: 0.308 Hom.: 1878

Bravo AF: 0.354

Asia WGS AF: 0.321 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs503397; hg19: chr11-126896977;