rs10494915

Variant names:

• chr1-209068535-A-G
• rs10494915
• XR_001738441.2:n.495+64219T>C

Variant summary

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

The XR_001738441.2(LOC107985255):​n.495+64219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,204 control chromosomes in the GnomAD database, including 2,221 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 0.16 (2221 hom., cov: 33)
• Consequence: LOC107985255 XR_001738441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.63
• Publications: 5 publications found

Genes affected

LOC107985255 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.160 AC: 24336 AN: 152086 Hom.: 2215 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.160 AC: 24361 AN: 152204 Hom.: 2221 Cov.: 33 AF XY: 0.156 AC XY: 11608 AN XY: 74440

African (AFR) AF: 0.241 AC: 10001 AN: 41498

American (AMR) AF: 0.124 AC: 1900 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3464

East Asian (EAS) AF: 0.115 AC: 596 AN: 5186

South Asian (SAS) AF: 0.0927 AC: 447 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1136 AN: 10612

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9230 AN: 68014

Other (OTH) AF: 0.154 AC: 325 AN: 2106

Alfa AF: 0.140 Hom.: 898

Bravo AF: 0.165

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	15
DANN	Benign	0.77
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs10494915; hg19: chr1-209241880;