9-122468813-A-G

Position:

• chr9-122468813-A-G

Variant summary

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

The ENST00000431442.2(ENSG00000234156):​n.814A>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 0.632 in 152,050 control chromosomes in the GnomAD database, including 30,794 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 0.63 (30794 hom., cov: 32)
• Consequence: ENSG00000234156 ENST00000431442.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

ENSG00000234156 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1J2	XR_007061271.1	n.868A>G		non_coding_transcript_exon_variant	2/5
OR1J2	XR_007061272.1	n.487A>G		non_coding_transcript_exon_variant	3/5
OR1J2	XR_007061273.1	n.487A>G		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000431442.2	n.814A>G		non_coding_transcript_exon_variant	6/10	3
ENSG00000234156	ENST00000433572.3	n.848A>G		non_coding_transcript_exon_variant	7/7	3
ENSG00000234156	ENST00000650686.1	n.477A>G		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96107 AN: 151932 Hom.: 30780 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.632 AC: 96153 AN: 152050 Hom.: 30794 Cov.: 32 AF XY: 0.628 AC XY: 46649 AN XY: 74308

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.675

Alfa AF: 0.693 Hom.: 30194

Bravo AF: 0.635

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2778636; hg19: chr9-125231092;