ENST00000527984.1:n.237-478C>T

Variant names:

• chr11-34533644-G-A
• rs836132
• ENST00000527984.1:n.237-478C>T

Variant summary

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

The ENST00000527984.1(ENSG00000255271):​n.237-478C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 148,544 control chromosomes in the GnomAD database, including 1,426 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 0.13 (1426 hom., cov: 27)
• Consequence: ENSG00000255271 ENST00000527984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 8 publications found

Genes affected

ENSG00000255271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527984.1. 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
	ENSG00000255271	ENST00000527984.1	TSL:2	n.237-478C>T		intron	N/A
	ENSG00000301952	ENST00000783043.1		n.201-2521G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 18652 AN: 148426 Hom.: 1421 Cov.: 27

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.126 AC: 18677 AN: 148544 Hom.: 1426 Cov.: 27 AF XY: 0.124 AC XY: 8963 AN XY: 72242

African (AFR) AF: 0.129 AC: 5163 AN: 39916

American (AMR) AF: 0.133 AC: 1959 AN: 14764

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 326 AN: 3438

East Asian (EAS) AF: 0.401 AC: 2027 AN: 5052

South Asian (SAS) AF: 0.0860 AC: 392 AN: 4556

European-Finnish (FIN) AF: 0.0508 AC: 519 AN: 10216

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7869 AN: 67364

Other (OTH) AF: 0.147 AC: 302 AN: 2048

Alfa AF: 0.126 Hom.: 5694

Bravo AF: 0.137

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.55
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs836132; hg19: chr11-34555191;