rs1928623

Positions:

• chr9-122546730-C-A
• chr9-122546730-C-G
• chr9-122546730-C-T

Variant summary

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

The ENST00000431442.2(ENSG00000234156):​n.1362+43860C>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 0.76 in 152,120 control chromosomes in the GnomAD database, including 44,509 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 0.76 (44509 hom., cov: 33)
• Consequence: ENST00000431442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1L8	XM_017014285.2	c.*23-201G>T		intron_variant			XP_016869774.1
OR1J2	XR_007061271.1	n.1541-33223C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000431442.2	n.1362+43860C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115486 AN: 152002 Hom.: 44463 Cov.: 33

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.760 AC: 115587 AN: 152120 Hom.: 44509 Cov.: 33 AF XY: 0.762 AC XY: 56613 AN XY: 74342

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.784

Alfa AF: 0.709 Hom.: 4833

Bravo AF: 0.772

Asia WGS AF: 0.901 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928623; hg19: chr9-125309009;