9-122487205-G-A

Position:

• chr9-122487205-G-A

Variant summary

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

The ENST00000431442.2(ENSG00000234156):​n.1187-15490G>A 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 0.637 in 152,034 control chromosomes in the GnomAD database, including 32,555 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 0.64 (32555 hom., cov: 31)
• Consequence: ENST00000431442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1J2	XM_024447516.2	c.-189-15490G>A		intron_variant			XP_024303284.1
OR1J2	XM_024447517.2	c.-107+11390G>A		intron_variant			XP_024303285.1
OR1J2	XR_007061271.1	n.1364+11390G>A		intron_variant, non_coding_transcript_variant
OR1J2	XR_007061274.1	n.1598-393G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000431442.2	n.1187-15490G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96732 AN: 151918 Hom.: 32492 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.637 AC: 96861 AN: 152034 Hom.: 32555 Cov.: 31 AF XY: 0.639 AC XY: 47487 AN XY: 74304

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.593

Alfa AF: 0.583 Hom.: 11058

Bravo AF: 0.645

Asia WGS AF: 0.637 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837971; hg19: chr9-125249484;