rs2732550

Variant names:

• chr11-35066771-T-G
• rs2732550
• ENST00000685560.2:n.159A>C

Variant summary

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

The ENST00000685560.2(ENSG00000289526):​n.159A>C 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 0.678 in 151,494 control chromosomes in the GnomAD database, including 36,132 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 (36132 hom., cov: 28)
• Consequence: ENSG00000289526 ENST00000685560.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289526	ENST00000685560.2		n.159A>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000289526	ENST00000687081.2		n.422A>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000289526	ENST00000701115.2		n.378A>C		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102539 AN: 151376 Hom.: 36085 Cov.: 28

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.678 AC: 102639 AN: 151494 Hom.: 36132 Cov.: 28 AF XY: 0.680 AC XY: 50328 AN XY: 74022

African (AFR) AF: 0.872 AC: 35968 AN: 41262

American (AMR) AF: 0.672 AC: 10227 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2225 AN: 3462

East Asian (EAS) AF: 0.790 AC: 4062 AN: 5142

South Asian (SAS) AF: 0.781 AC: 3733 AN: 4780

European-Finnish (FIN) AF: 0.545 AC: 5709 AN: 10480

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38540 AN: 67848

Other (OTH) AF: 0.688 AC: 1448 AN: 2106

Alfa AF: 0.627 Hom.: 3841

Bravo AF: 0.693

Asia WGS AF: 0.776 AC: 2696 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2732550; hg19: chr11-35088318;