chr9-21188271-T-C

Position:

• chr9-21188271-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 0.201 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/exons	MANE	UniProt

Ensembl

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