rs11073059

Variant names:

• chr15-34697473-T-A
• rs11073059
• ENST00000720751.1:n.235-21840A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-34697473-T-A
• chr15-34697473-T-C
• chr15-34697473-T-G

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.235-21840A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,050 control chromosomes in the GnomAD database, including 12,826 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 0.41 (12826 hom., cov: 33)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860
• Publications: 8 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720751.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294065	ENST00000720751.1		n.235-21840A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62058 AN: 151932 Hom.: 12822 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.408 AC: 62093 AN: 152050 Hom.: 12826 Cov.: 33 AF XY: 0.407 AC XY: 30243 AN XY: 74336

African (AFR) AF: 0.378 AC: 15693 AN: 41480

American (AMR) AF: 0.373 AC: 5693 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1196 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2276 AN: 5174

South Asian (SAS) AF: 0.589 AC: 2839 AN: 4818

European-Finnish (FIN) AF: 0.347 AC: 3662 AN: 10562

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29204 AN: 67954

Other (OTH) AF: 0.405 AC: 853 AN: 2108

Alfa AF: 0.405 Hom.: 1569

Bravo AF: 0.405

Asia WGS AF: 0.515 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.37
PhyloP100		-0.86

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11073059;

hg19: chr15-34989674;