rs17259784

Variant names:

• chr1-208584241-G-C
• rs17259784
• ENST00000846586.1:n.139-29173G>C

Variant summary

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

The ENST00000846586.1(ENSG00000310018):​n.139-29173G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,206 control chromosomes in the GnomAD database, including 1,488 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 0.12 (1488 hom., cov: 32)
• Consequence: ENSG00000310018 ENST00000846586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 13 publications found

Genes affected

ENSG00000310018 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846586.1. 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
	ENSG00000310018	ENST00000846586.1		n.139-29173G>C		intron	N/A
	ENSG00000310018	ENST00000846587.1		n.119-29173G>C		intron	N/A
	ENSG00000310018	ENST00000846588.1		n.119-23115G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18994 AN: 152088 Hom.: 1493 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.125 AC: 18989 AN: 152206 Hom.: 1488 Cov.: 32 AF XY: 0.124 AC XY: 9264 AN XY: 74422

African (AFR) AF: 0.0486 AC: 2022 AN: 41566

American (AMR) AF: 0.104 AC: 1593 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3464

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.152 AC: 735 AN: 4820

European-Finnish (FIN) AF: 0.171 AC: 1808 AN: 10586

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11760 AN: 67988

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.158 Hom.: 1125

Bravo AF: 0.114

Asia WGS AF: 0.0740 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.65
PhyloP100		-0.55

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: rs17259784;

hg19: chr1-208757586;

COSMIC: COSV60020952;