chr9-75505412-G-T

Variant names:

• chr9-75505412-G-T
• rs10512043

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 0.164 in 151,554 control chromosomes in the GnomAD database, including 2,448 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 0.16 (2448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 3 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 = 0.383 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: 0.164 AC: 24792 AN: 151436 Hom.: 2447 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.164 AC: 24787 AN: 151554 Hom.: 2448 Cov.: 32 AF XY: 0.164 AC XY: 12129 AN XY: 74054

African (AFR) AF: 0.0688 AC: 2845 AN: 41380

American (AMR) AF: 0.167 AC: 2531 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3460

East Asian (EAS) AF: 0.398 AC: 2038 AN: 5124

South Asian (SAS) AF: 0.143 AC: 688 AN: 4816

European-Finnish (FIN) AF: 0.199 AC: 2096 AN: 10548

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13399 AN: 67740

Other (OTH) AF: 0.177 AC: 373 AN: 2102

Alfa AF: 0.184 Hom.: 4467

Bravo AF: 0.163

Asia WGS AF: 0.244 AC: 846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10512043; hg19: chr9-78120328;