chr9-132375086-A-G

Position:

• chr9-132375086-A-G

Variant summary

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

The XR_007061827.1(LOC124902292):​n.190A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,090 control chromosomes in the GnomAD database, including 3,000 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 0.19 (3000 hom., cov: 32)
• Consequence: LOC124902292 XR_007061827.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

LOC124902292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902292	XR_007061827.1	n.190A>G		non_coding_transcript_exon_variant	2/2
LOC124902292	XR_007061828.1	n.190A>G		non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29614 AN: 151972 Hom.: 3001 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.195 AC: 29624 AN: 152090 Hom.: 3000 Cov.: 32 AF XY: 0.195 AC XY: 14464 AN XY: 74350

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.197

Alfa AF: 0.188 Hom.: 2814

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7030233; hg19: chr9-135250473; COSMIC: COSV57502979;