11-35073939-A-G

Variant names:

• chr11-35073939-A-G
• rs2732540
• ENST00000748188.1:n.46T>C

Variant summary

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

The ENST00000748188.1(ENSG00000289526):​n.46T>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 0.599 in 152,036 control chromosomes in the GnomAD database, including 27,551 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 0.60 (27551 hom., cov: 32)
• Consequence: ENSG00000289526 ENST00000748188.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289526	ENST00000748188.1	n.46T>C		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000289526	ENST00000748189.1	n.50T>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000297460	ENST00000747995.1	n.136+11100A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90915 AN: 151918 Hom.: 27514 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.599 AC: 90999 AN: 152036 Hom.: 27551 Cov.: 32 AF XY: 0.603 AC XY: 44836 AN XY: 74306

African (AFR) AF: 0.619 AC: 25639 AN: 41452

American (AMR) AF: 0.639 AC: 9759 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.791 AC: 4100 AN: 5184

South Asian (SAS) AF: 0.780 AC: 3764 AN: 4826

European-Finnish (FIN) AF: 0.538 AC: 5677 AN: 10552

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37816 AN: 67952

Other (OTH) AF: 0.622 AC: 1315 AN: 2114

Alfa AF: 0.454 Hom.: 1283

Bravo AF: 0.603

Asia WGS AF: 0.762 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.53
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2732540; hg19: chr11-35095486;