10-89204269-A-G

Variant names:

• chr10-89204269-A-G
• rs17117126
• XR_946180.4:n.356-162A>G

Variant summary

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

The XR_946180.4(LOC105378418):​n.356-162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,002 control chromosomes in the GnomAD database, including 3,095 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 0.14 (3095 hom., cov: 32)
• Consequence: LOC105378418 XR_946180.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 7 publications found

Genes affected

LOC105378418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20630 AN: 151884 Hom.: 3084 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.136 AC: 20661 AN: 152002 Hom.: 3095 Cov.: 32 AF XY: 0.148 AC XY: 10985 AN XY: 74280

African (AFR) AF: 0.0249 AC: 1033 AN: 41558

American (AMR) AF: 0.217 AC: 3311 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3908 AN: 5158

South Asian (SAS) AF: 0.323 AC: 1557 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2522 AN: 10526

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7303 AN: 67880

Other (OTH) AF: 0.141 AC: 298 AN: 2110

Alfa AF: 0.119 Hom.: 2588

Bravo AF: 0.132

Asia WGS AF: 0.457 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.55
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs17117126; hg19: chr10-90964026;