rs17587100

Variant names:

• chr2-118080834-A-C
• rs17587100
• ENST00000747789.1:n.231+6679T>G

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+6679T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 152,258 control chromosomes in the GnomAD database, including 509 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 0.068 (509 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 14 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747789.1. 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
	ENSG00000297418	ENST00000747789.1		n.231+6679T>G		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+7417T>G		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.272-6281T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10363 AN: 152140 Hom.: 504 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0606

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0683 AC: 10396 AN: 152258 Hom.: 509 Cov.: 32 AF XY: 0.0740 AC XY: 5512 AN XY: 74440

African (AFR) AF: 0.0226 AC: 938 AN: 41558

American (AMR) AF: 0.105 AC: 1609 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0606 AC: 210 AN: 3468

East Asian (EAS) AF: 0.0403 AC: 209 AN: 5182

South Asian (SAS) AF: 0.0663 AC: 320 AN: 4824

European-Finnish (FIN) AF: 0.175 AC: 1856 AN: 10594

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0732 AC: 4976 AN: 68014

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0639 Hom.: 570

Bravo AF: 0.0612

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.58
PhyloP100		0.56

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: rs17587100;

hg19: chr2-118838410;

COSMIC: COSV60100147;