chr17-13086069-C-G

Variant names:

• chr17-13086069-C-G
• rs11652547
• ENST00000808889.1:n.921-14245C>G

Variant summary

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

The ENST00000808889.1(ENSG00000273098):​n.921-14245C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,902 control chromosomes in the GnomAD database, including 9,394 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 0.35 (9394 hom., cov: 31)
• Consequence: ENSG00000273098 ENST00000808889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 2 publications found

Genes affected

ENSG00000273098 (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 (AMR) allele frequency at 95% confidence interval = 0.427 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
ENSG00000273098	ENST00000808889.1	n.921-14245C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52843 AN: 151784 Hom.: 9387 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.348 AC: 52886 AN: 151902 Hom.: 9394 Cov.: 31 AF XY: 0.355 AC XY: 26337 AN XY: 74216

African (AFR) AF: 0.309 AC: 12807 AN: 41442

American (AMR) AF: 0.435 AC: 6642 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1764 AN: 5138

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4816

European-Finnish (FIN) AF: 0.400 AC: 4207 AN: 10530

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23667 AN: 67926

Other (OTH) AF: 0.344 AC: 728 AN: 2114

Alfa AF: 0.352 Hom.: 1183

Bravo AF: 0.349

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.29
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs11652547; hg19: chr17-12989386;