9-102105556-C-T

Variant names:

• chr9-102105556-C-T
• rs10989824

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 0.112 in 151,144 control chromosomes in the GnomAD database, including 1,847 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 0.11 (1847 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 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: 0.112 AC: 16853 AN: 151026 Hom.: 1844 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0214

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.0481

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.0945

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

GnomAD4 genome AF: 0.112 AC: 16868 AN: 151144 Hom.: 1847 Cov.: 32 AF XY: 0.121 AC XY: 8961 AN XY: 73820

African (AFR) AF: 0.123 AC: 5077 AN: 41336

American (AMR) AF: 0.171 AC: 2589 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.0214 AC: 74 AN: 3460

East Asian (EAS) AF: 0.599 AC: 3056 AN: 5102

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4814

European-Finnish (FIN) AF: 0.0958 AC: 1010 AN: 10538

Middle Eastern (MID) AF: 0.0414 AC: 12 AN: 290

European-Non Finnish (NFE) AF: 0.0514 AC: 3466 AN: 67482

Other (OTH) AF: 0.101 AC: 212 AN: 2096

Alfa AF: 0.0820 Hom.: 1827

Bravo AF: 0.118

Asia WGS AF: 0.419 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.7
DANN	Benign	0.78
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10989824; hg19: chr9-104867838;