9-97407238-G-T

Variant names:

• chr9-97407238-G-T
• rs1462090
• ENST00000667253.1:n.52-2448C>A

Variant summary

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

The ENST00000667253.1(ENSG00000286375):​n.52-2448C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,070 control chromosomes in the GnomAD database, including 7,463 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 (7463 hom., cov: 32)
• Consequence: ENSG00000286375 ENST00000667253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

ENSG00000286375 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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	ENST00000667253.1	n.52-2448C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47434 AN: 151952 Hom.: 7454 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.312 AC: 47466 AN: 152070 Hom.: 7463 Cov.: 32 AF XY: 0.310 AC XY: 23064 AN XY: 74334

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.318

Alfa AF: 0.308 Hom.: 3708

Bravo AF: 0.314

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.099
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1462090; hg19: chr9-100169520;