chr11-35066771-T-G

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376626	XR_001748180.2	n.421A>C		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105376626	XR_007062653.1	n.421A>C		non_coding_transcript_exon_variant	Exon 1 of 5
LOC105376626	XR_007062654.1	n.421A>C		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.159A>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289526	ENST00000687081.2	n.422A>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000289526	ENST00000701115.2	n.378A>C		non_coding_transcript_exon_variant	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 v4.3

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs2732550; hg19: chr11-35088318;