9-21153107-T-C

Variant names:

• chr9-21153107-T-C
• rs10964863

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 0.687 in 152,078 control chromosomes in the GnomAD database, including 36,509 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 0.69 (36509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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: 0.687 AC: 104443 AN: 151958 Hom.: 36473 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.687 AC: 104535 AN: 152078 Hom.: 36509 Cov.: 32 AF XY: 0.684 AC XY: 50859 AN XY: 74326

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.693

Alfa AF: 0.632 Hom.: 6012

Bravo AF: 0.700

Asia WGS AF: 0.718 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.017
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10964863; hg19: chr9-21153106; COSMIC: COSV69450693;