rs1860189

Variant names:

• chr17-34251339-A-G
• rs1860189
• ENST00000776537.1:n.238+534T>C

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+534T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,196 control chromosomes in the GnomAD database, including 1,793 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 0.15 (1793 hom., cov: 32)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 8 publications found

Genes affected

ENSG00000301139 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 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
ENSG00000301139	ENST00000776537.1	n.238+534T>C		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.238+534T>C		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.236+534T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22748 AN: 152078 Hom.: 1793 Cov.: 32

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.149 AC: 22740 AN: 152196 Hom.: 1793 Cov.: 32 AF XY: 0.150 AC XY: 11149 AN XY: 74400

African (AFR) AF: 0.0905 AC: 3757 AN: 41512

American (AMR) AF: 0.145 AC: 2219 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.184 AC: 953 AN: 5176

South Asian (SAS) AF: 0.161 AC: 779 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1736 AN: 10604

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11973 AN: 67996

Other (OTH) AF: 0.165 AC: 348 AN: 2112

Alfa AF: 0.156 Hom.: 312

Bravo AF: 0.146

Asia WGS AF: 0.167 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.44
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs1860189; hg19: chr17-32578358;