9-101846453-T-C

Variant names:

• chr9-101846453-T-C
• rs10512292
• XR_930187.3:n.134+2118A>G

Variant summary

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

The XR_930187.3(LOC105376187):​n.134+2118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,248 control chromosomes in the GnomAD database, including 451 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 0.056 (451 hom., cov: 32)
• Consequence: LOC105376187 XR_930187.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 0 publications found

Genes affected

LOC105376187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 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: 0.0562 AC: 8545 AN: 152130 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0562 AC: 8560 AN: 152248 Hom.: 451 Cov.: 32 AF XY: 0.0564 AC XY: 4199 AN XY: 74432

African (AFR) AF: 0.128 AC: 5331 AN: 41554

American (AMR) AF: 0.0330 AC: 504 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.130 AC: 672 AN: 5170

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4824

European-Finnish (FIN) AF: 0.0212 AC: 225 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0204 AC: 1388 AN: 68014

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0429 Hom.: 38

Bravo AF: 0.0598

Asia WGS AF: 0.101 AC: 353 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.76
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10512292; hg19: chr9-104608735;