rs9332460

chr9-122473276-A-Gchr9-122473276-A-T

Variant summary

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

The ENST00000431442.2(ENSG00000234156):n.1186+4091A>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 0.259 in 152,084 control chromosomes in the GnomAD database, including 5,814 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 0.26 (5814 hom., cov: 32)
• Consequence: ENST00000431442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR1J2	XM_024447516.2	c.-190+4091A>G		intron_variant
OR1J2	XM_024447517.2	c.-230-2416A>G		intron_variant
OR1J2	XR_007061271.1	n.1241-2416A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000431442.2	n.1186+4091A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000412262.2	n.57-1802A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000650686.1	n.850-2416A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39391 AN: 151966 Hom.: 5789 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.259 AC: 39464 AN: 152084 Hom.: 5814 Cov.: 32 AF XY: 0.261 AC XY: 19408 AN XY: 74348

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.215

Alfa AF: 0.225 Hom.: 868

Bravo AF: 0.254

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.52
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332460; hg19: chr9-125235555;