rs2732549

Variant names:

• chr11-35066852-G-A
• rs2732549
• ENST00000685560.2:n.78C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-35066852-G-A
• chr11-35066852-G-C

Variant summary

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

The ENST00000685560.2(ENSG00000289526):​n.78C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,830 control chromosomes in the GnomAD database, including 37,021 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 0.68 (37021 hom., cov: 30)
• Consequence: ENSG00000289526 ENST00000685560.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 23 publications found

Genes affected

ENSG00000289526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685560.2. 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
	ENSG00000289526	ENST00000685560.2		n.78C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000289526	ENST00000687081.2		n.341C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000289526	ENST00000701115.2		n.297C>T		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103343 AN: 151712 Hom.: 36964 Cov.: 30

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.681 AC: 103453 AN: 151830 Hom.: 37021 Cov.: 30 AF XY: 0.684 AC XY: 50716 AN XY: 74166

African (AFR) AF: 0.906 AC: 37524 AN: 41432

American (AMR) AF: 0.669 AC: 10196 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2206 AN: 3468

East Asian (EAS) AF: 0.791 AC: 4065 AN: 5142

South Asian (SAS) AF: 0.779 AC: 3746 AN: 4810

European-Finnish (FIN) AF: 0.538 AC: 5659 AN: 10524

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37899 AN: 67908

Other (OTH) AF: 0.682 AC: 1432 AN: 2100

Alfa AF: 0.596 Hom.: 33291

Bravo AF: 0.697

Asia WGS AF: 0.777 AC: 2704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.6
DANN	Benign	0.53
PhyloP100		0.79

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: rs2732549;

hg19: chr11-35088399;