rs10512292

chr9-101846453-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_930187.3(LOC105376187):n.134+2118A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

LOC105376187 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376187	XR_930187.3	n.134+2118A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0212

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0392 Hom.: 30

Bravo AF: 0.0598

Asia WGS AF: 0.101 AC: 353 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.9
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512292; hg19: chr9-104608735;