9-21350079-A-T

Position:

• chr9-21350079-A-T

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 0.182 in 228,022 control chromosomes in the GnomAD database, including 4,071 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 0.18 (2611 hom., cov: 32)
  • Exomes 𝑓: 0.19 (1460 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27411 AN: 152102 Hom.: 2609 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.187 AC: 14171 AN: 75802 Hom.: 1460 Cov.: 2 AF XY: 0.186 AC XY: 7280 AN XY: 39198

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.247

Gnomad4 ASJ exome AF: 0.196

Gnomad4 EAS exome AF: 0.308

Gnomad4 SAS exome AF: 0.119

Gnomad4 FIN exome AF: 0.197

Gnomad4 NFE exome AF: 0.172

Gnomad4 OTH exome AF: 0.193

GnomAD4 genome AF: 0.180 AC: 27428 AN: 152220 Hom.: 2611 Cov.: 32 AF XY: 0.182 AC XY: 13548 AN XY: 74426

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.181

Alfa AF: 0.0986 Hom.: 143

Bravo AF: 0.186

Asia WGS AF: 0.189 AC: 656 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2990144; hg19: chr9-21350078;