9-90093138-T-C

Variant names:

• chr9-90093138-T-C
• rs10123553

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.13

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;