rs1352864

Variant names:

• chr11-27845236-C-A
• rs1352864
• ENST00000530663.1:n.147+32266G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-27845236-C-A
• chr11-27845236-C-G

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.147+32266G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,016 control chromosomes in the GnomAD database, including 52,492 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 0.83 (52492 hom., cov: 31)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 2 publications found

Genes affected

ENSG00000255496 (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 (NFE) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530663.1. 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
	ENSG00000255496	ENST00000530663.1	TSL:1	n.147+32266G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125908 AN: 151898 Hom.: 52452 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.829 AC: 125996 AN: 152016 Hom.: 52492 Cov.: 31 AF XY: 0.830 AC XY: 61700 AN XY: 74310

African (AFR) AF: 0.799 AC: 33136 AN: 41446

American (AMR) AF: 0.793 AC: 12102 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3084 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3451 AN: 5154

South Asian (SAS) AF: 0.751 AC: 3611 AN: 4808

European-Finnish (FIN) AF: 0.938 AC: 9944 AN: 10604

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57856 AN: 67958

Other (OTH) AF: 0.850 AC: 1792 AN: 2108

Alfa AF: 0.842 Hom.: 232994

Bravo AF: 0.818

Asia WGS AF: 0.733 AC: 2550 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	0.24
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1352864;

hg19: chr11-27866783;