11-35063045-T-C

Variant names:

• chr11-35063045-T-C
• rs2732552
• ENST00000748194.1:n.719A>G

Variant summary

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

The ENST00000748194.1(ENSG00000289526):​n.719A>G 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 0.516 in 152,026 control chromosomes in the GnomAD database, including 21,246 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 0.52 (21246 hom., cov: 32)
• Consequence: ENSG00000289526 ENST00000748194.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 18 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 (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748194.1. 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	ENST00000748194.1		n.719A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000289526	ENST00000748195.1		n.1646A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000289526	ENST00000685560.2		n.443+2075A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78464 AN: 151910 Hom.: 21241 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.516 AC: 78482 AN: 152026 Hom.: 21246 Cov.: 32 AF XY: 0.521 AC XY: 38733 AN XY: 74316

African (AFR) AF: 0.352 AC: 14582 AN: 41466

American (AMR) AF: 0.607 AC: 9285 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3889 AN: 5168

South Asian (SAS) AF: 0.690 AC: 3323 AN: 4816

European-Finnish (FIN) AF: 0.522 AC: 5508 AN: 10558

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37908 AN: 67954

Other (OTH) AF: 0.551 AC: 1164 AN: 2112

Alfa AF: 0.546 Hom.: 62378

Bravo AF: 0.513

Asia WGS AF: 0.687 AC: 2390 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	3.3
DANN	Benign	0.60
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs2732552; hg19: chr11-35084592;