rs10757189

Variant names:

• chr9-21142605-G-A
• rs10757189

Your query was ambiguous. Multiple possible variants found:

• chr9-21142605-G-A
• chr9-21142605-G-T

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 0.264 in 151,978 control chromosomes in the GnomAD database, including 5,366 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 0.26 (5366 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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: 0.264 AC: 40144 AN: 151860 Hom.: 5366 Cov.: 31

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.264 AC: 40165 AN: 151978 Hom.: 5366 Cov.: 31 AF XY: 0.261 AC XY: 19350 AN XY: 74260

African (AFR) AF: 0.238 AC: 9855 AN: 41434

American (AMR) AF: 0.311 AC: 4742 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1939 AN: 5166

South Asian (SAS) AF: 0.261 AC: 1255 AN: 4806

European-Finnish (FIN) AF: 0.195 AC: 2054 AN: 10560

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18219 AN: 67964

Other (OTH) AF: 0.277 AC: 584 AN: 2106

Alfa AF: 0.268 Hom.: 8732

Bravo AF: 0.275

Asia WGS AF: 0.330 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.76
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs10757189; hg19: chr9-21142604; COSMIC: COSV66522379;