9-21188271-T-C

Variant names:

• chr9-21188271-T-C
• rs10964898

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 0.201 in 152,062 control chromosomes in the GnomAD database, including 3,352 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 0.20 (3352 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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: 0.201 AC: 30576 AN: 151944 Hom.: 3349 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.201 AC: 30611 AN: 152062 Hom.: 3352 Cov.: 33 AF XY: 0.202 AC XY: 15003 AN XY: 74322

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.198

Alfa AF: 0.193 Hom.: 351

Bravo AF: 0.208

Asia WGS AF: 0.249 AC: 864 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.67
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10964898; hg19: chr9-21188270;