9-21228766-A-T

Variant names:

• chr9-21228766-A-T
• rs7858057

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.324 AC: 13433 AN: 41450

American (AMR) AF: 0.275 AC: 4200 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2687 AN: 5180

South Asian (SAS) AF: 0.185 AC: 895 AN: 4828

European-Finnish (FIN) AF: 0.193 AC: 2035 AN: 10544

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11497 AN: 67954

Other (OTH) AF: 0.219 AC: 462 AN: 2106

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
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs7858057; hg19: chr9-21228765;