chr9-90093138-T-C

Position:

• chr9-90093138-T-C

Variant summary

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

The variant allele was found at a frequency of 0.4 in 151,710 control chromosomes in the GnomAD database, including 12,494 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 0.40 (12494 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.13

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 (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90093138T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60659 AN: 151592 Hom.: 12482 Cov.: 30

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.400 AC: 60708 AN: 151710 Hom.: 12494 Cov.: 30 AF XY: 0.399 AC XY: 29603 AN XY: 74144

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.440

Alfa AF: 0.440 Hom.: 14025

Bravo AF: 0.397

Asia WGS AF: 0.340 AC: 1183 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	0.062
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10123553; hg19: chr9-92855420;