rs1462089

Variant names:

• chr9-97406082-C-G
• rs1462089
• ENST00000667253.2:n.65-1292G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667253.2(ENSG00000286375):​n.65-1292G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,086 control chromosomes in the GnomAD database, including 7,348 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 0.31 (7348 hom., cov: 32)
• Consequence: ENSG00000286375 ENST00000667253.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 2 publications found

Genes affected

ENSG00000286375 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286375	ENST00000667253.2	n.65-1292G>C		intron_variant	Intron 1 of 1
ENSG00000286375	ENST00000778879.1	n.58-4532G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47134 AN: 151968 Hom.: 7345 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.310 AC: 47156 AN: 152086 Hom.: 7348 Cov.: 32 AF XY: 0.308 AC XY: 22930 AN XY: 74348

African (AFR) AF: 0.339 AC: 14054 AN: 41462

American (AMR) AF: 0.275 AC: 4205 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1408 AN: 5174

South Asian (SAS) AF: 0.253 AC: 1222 AN: 4826

European-Finnish (FIN) AF: 0.273 AC: 2882 AN: 10568

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20911 AN: 67970

Other (OTH) AF: 0.315 AC: 665 AN: 2108

Alfa AF: 0.313 Hom.: 938

Bravo AF: 0.312

Asia WGS AF: 0.268 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1462089; hg19: chr9-100168364;