9-121803541-T-C

Variant names:

• chr9-121803541-T-C
• rs10760187

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 0.593 in 152,074 control chromosomes in the GnomAD database, including 28,147 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 0.59 (28147 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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: 0.592 AC: 90023 AN: 151956 Hom.: 28089 Cov.: 33

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.593 AC: 90134 AN: 152074 Hom.: 28147 Cov.: 33 AF XY: 0.593 AC XY: 44041 AN XY: 74324

African (AFR) AF: 0.785 AC: 32540 AN: 41466

American (AMR) AF: 0.456 AC: 6977 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4127 AN: 5182

South Asian (SAS) AF: 0.713 AC: 3433 AN: 4814

European-Finnish (FIN) AF: 0.489 AC: 5168 AN: 10572

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34171 AN: 67966

Other (OTH) AF: 0.557 AC: 1176 AN: 2112

Alfa AF: 0.572 Hom.: 7006

Bravo AF: 0.596

Asia WGS AF: 0.772 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10760187; hg19: chr9-124565820;