chr11-13069395-G-A

Variant names:

• chr11-13069395-G-A
• rs2727405
• ENST00000531136.1:n.48-14361C>T

Variant summary

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

The ENST00000531136.1(ENSG00000255558):​n.48-14361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,090 control chromosomes in the GnomAD database, including 8,730 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 0.33 (8730 hom., cov: 33)
• Consequence: ENSG00000255558 ENST00000531136.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 4 publications found

Genes affected

ENSG00000255558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531136.1. 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
	ENSG00000255558	ENST00000531136.1	TSL:3	n.48-14361C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50461 AN: 151972 Hom.: 8721 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.332 AC: 50513 AN: 152090 Hom.: 8730 Cov.: 33 AF XY: 0.337 AC XY: 25075 AN XY: 74330

African (AFR) AF: 0.406 AC: 16845 AN: 41460

American (AMR) AF: 0.337 AC: 5161 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3470

East Asian (EAS) AF: 0.534 AC: 2746 AN: 5146

South Asian (SAS) AF: 0.416 AC: 2008 AN: 4828

European-Finnish (FIN) AF: 0.301 AC: 3184 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18609 AN: 67984

Other (OTH) AF: 0.308 AC: 651 AN: 2116

Alfa AF: 0.289 Hom.: 24416

Bravo AF: 0.335

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.63
DANN	Benign	0.43
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2727405; hg19: chr11-13090942;