11-127027082-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000255087 (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 = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530177.2. 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
	ENSG00000255087	ENST00000530177.2	TSL:4	n.154+5175C>T		intron	N/A
	ENSG00000255087	ENST00000647195.1		n.143+5175C>T		intron	N/A
	ENSG00000255087	ENST00000654157.1		n.150+5175C>T		intron	N/A

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

African (AFR) AF: 0.480 AC: 19907 AN: 41478

American (AMR) AF: 0.318 AC: 4861 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1247 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1971 AN: 5156

South Asian (SAS) AF: 0.326 AC: 1572 AN: 4822

European-Finnish (FIN) AF: 0.377 AC: 3988 AN: 10580

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19324 AN: 68008

Other (OTH) AF: 0.324 AC: 684 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.47
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs503397; hg19: chr11-126896977;