rs10178489

Variant names:

• chr2-17871407-C-G
• rs10178489
• XR_007086226.1:n.1199-2666G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-17871407-C-G
• chr2-17871407-C-T

Variant summary

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

The XR_007086226.1(LOC124907737):​n.1199-2666G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,118 control chromosomes in the GnomAD database, including 6,885 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 0.30 (6885 hom., cov: 32)
• Consequence: LOC124907737 XR_007086226.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 5 publications found

Genes affected

LOC124907737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45107 AN: 152000 Hom.: 6884 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.297 AC: 45127 AN: 152118 Hom.: 6885 Cov.: 32 AF XY: 0.296 AC XY: 21969 AN XY: 74336

African (AFR) AF: 0.347 AC: 14394 AN: 41494

American (AMR) AF: 0.254 AC: 3885 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1119 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2015 AN: 5180

South Asian (SAS) AF: 0.184 AC: 887 AN: 4830

European-Finnish (FIN) AF: 0.282 AC: 2983 AN: 10564

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18820 AN: 67974

Other (OTH) AF: 0.298 AC: 629 AN: 2112

Alfa AF: 0.267 Hom.: 704

Bravo AF: 0.301

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.55
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10178489; hg19: chr2-18052674;