9-21228766-A-T

Variant names:

• chr9-21228766-A-T
• rs7858057

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 0.237 in 152,014 control chromosomes in the GnomAD database, including 4,975 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 0.24 (4975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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: 0.237 AC: 36053 AN: 151898 Hom.: 4969 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.237 AC: 36088 AN: 152014 Hom.: 4975 Cov.: 32 AF XY: 0.239 AC XY: 17748 AN XY: 74320

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.219

Alfa AF: 0.212 Hom.: 453

Bravo AF: 0.249

Asia WGS AF: 0.325 AC: 1124 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7858057; hg19: chr9-21228765;