rs2727405

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-13069395-G-A
• chr11-13069395-G-C
• chr11-13069395-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000255558 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000255558	ENST00000531136.1	n.48-14361C>T		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.308

Alfa AF: 0.281 Hom.: 9772

Bravo AF: 0.335

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2727405; hg19: chr11-13090942;