9-21153107-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;