9-90093138-T-C

Variant names:

• chr9-90093138-T-C
• rs10123553

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.325 AC: 13439 AN: 41344

American (AMR) AF: 0.400 AC: 6101 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1797 AN: 3462

East Asian (EAS) AF: 0.366 AC: 1879 AN: 5130

South Asian (SAS) AF: 0.268 AC: 1279 AN: 4770

European-Finnish (FIN) AF: 0.433 AC: 4573 AN: 10568

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30238 AN: 67876

Other (OTH) AF: 0.440 AC: 924 AN: 2098

Alfa AF: 0.435 Hom.: 18023

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
PhyloP100		-7.1

Splicing

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

Other links and lift over

dbSNP: rs10123553; hg19: chr9-92855420;