rs11073060

Variant names:

• chr15-34697650-C-A
• rs11073060
• ENST00000720751.1:n.235-22017G>T

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.235-22017G>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 151,918 control chromosomes in the GnomAD database, including 12,786 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 (12786 hom., cov: 32)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 13 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 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.235-22017G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61926 AN: 151800 Hom.: 12782 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.408 AC: 61961 AN: 151918 Hom.: 12786 Cov.: 32 AF XY: 0.406 AC XY: 30178 AN XY: 74258

African (AFR) AF: 0.377 AC: 15621 AN: 41420

American (AMR) AF: 0.372 AC: 5681 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2240 AN: 5124

South Asian (SAS) AF: 0.588 AC: 2832 AN: 4816

European-Finnish (FIN) AF: 0.347 AC: 3665 AN: 10554

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

European-Non Finnish (NFE) AF: 0.430 AC: 29194 AN: 67958

Other (OTH) AF: 0.405 AC: 855 AN: 2110

Alfa AF: 0.420 Hom.: 21388

Bravo AF: 0.404

Asia WGS AF: 0.513 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.4
DANN	Benign	0.33
PhyloP100		0.20

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: rs11073060;

hg19: chr15-34989851;

COSMIC: COSV69022330;