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: 22 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376626	XR_001748180.2	n.340C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105376626	XR_007062653.1	n.340C>T		non_coding_transcript_exon_variant	Exon 1 of 5
LOC105376626	XR_007062654.1	n.340C>T		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289526	ENST00000685560.2	n.78C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289526	ENST00000687081.2	n.341C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000289526	ENST00000701115.2	n.297C>T		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs2732549; hg19: chr11-35088399;