chr9-21143021-C-T

Variant names:

• chr9-21143021-C-T
• rs10511694

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.288 in 151,870 control chromosomes in the GnomAD database, including 6,414 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 0.29 (6414 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

ACMG classification

Verdict is Benign. Variant got -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 = 0.431 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: 0.288 AC: 43713 AN: 151750 Hom.: 6414 Cov.: 30

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.288 AC: 43738 AN: 151870 Hom.: 6414 Cov.: 30 AF XY: 0.286 AC XY: 21234 AN XY: 74222

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.299

Alfa AF: 0.274 Hom.: 966

Bravo AF: 0.299

Asia WGS AF: 0.383 AC: 1329 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	1.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511694; hg19: chr9-21143020; COSMIC: COSV66522383;