chr17-14501349-T-C

Variant names:

• chr17-14501349-T-C
• rs2080115
• ENST00000700765.2:n.439-24836T>C

Variant summary

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

The ENST00000700765.2(ENSG00000230647):​n.439-24836T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,022 control chromosomes in the GnomAD database, including 3,067 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 0.20 (3067 hom., cov: 32)
• Consequence: ENSG00000230647 ENST00000700765.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 4 publications found

Genes affected

ENSG00000230647 (HGNC:58488):

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 (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000700765.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230647	ENST00000700765.2		n.439-24836T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30205 AN: 151904 Hom.: 3066 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.199 AC: 30206 AN: 152022 Hom.: 3067 Cov.: 32 AF XY: 0.203 AC XY: 15053 AN XY: 74290

African (AFR) AF: 0.187 AC: 7746 AN: 41488

American (AMR) AF: 0.162 AC: 2474 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5164

South Asian (SAS) AF: 0.212 AC: 1024 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2949 AN: 10524

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13767 AN: 67958

Other (OTH) AF: 0.184 AC: 388 AN: 2106

Alfa AF: 0.190 Hom.: 5356

Bravo AF: 0.185

Asia WGS AF: 0.209 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.089
DANN	Benign	0.79
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2080115; hg19: chr17-14404666; COSMIC: COSV60075364;