9-75687692-C-T

Variant names:

• chr9-75687692-C-T
• rs10512050

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 0.28 in 151,916 control chromosomes in the GnomAD database, including 6,433 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 0.28 (6433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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: 0.280 AC: 42477 AN: 151798 Hom.: 6420 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.280 AC: 42531 AN: 151916 Hom.: 6433 Cov.: 32 AF XY: 0.276 AC XY: 20496 AN XY: 74222

African (AFR) AF: 0.371 AC: 15376 AN: 41426

American (AMR) AF: 0.213 AC: 3253 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3468

East Asian (EAS) AF: 0.0517 AC: 266 AN: 5146

South Asian (SAS) AF: 0.180 AC: 867 AN: 4806

European-Finnish (FIN) AF: 0.287 AC: 3023 AN: 10546

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17991 AN: 67956

Other (OTH) AF: 0.254 AC: 535 AN: 2108

Alfa AF: 0.248 Hom.: 2554

Bravo AF: 0.277

Asia WGS AF: 0.106 AC: 368 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10512050; hg19: chr9-78302608;