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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+7417T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747789.1	n.231+6679T>G		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.104+7417T>G		intron_variant	Intron 1 of 2
ENSG00000297418	ENST00000747791.1	n.272-6281T>G		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs17587100; hg19: chr2-118838410; COSMIC: COSV60100147;