9-21218874-A-T

Variant names:

• chr9-21218874-A-T
• rs1820314

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 0.279 in 151,632 control chromosomes in the GnomAD database, including 6,534 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 0.28 (6534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 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: 0.279 AC: 42315 AN: 151514 Hom.: 6524 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.279 AC: 42368 AN: 151632 Hom.: 6534 Cov.: 32 AF XY: 0.279 AC XY: 20659 AN XY: 74130

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.269

Alfa AF: 0.255 Hom.: 658

Bravo AF: 0.294

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1820314; hg19: chr9-21218873;