9-69021734-A-T

Variant names:

• chr9-69021734-A-T
• rs1590944

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 0.228 in 152,014 control chromosomes in the GnomAD database, including 4,251 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 0.23 (4251 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34549 AN: 151896 Hom.: 4240 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.228 AC: 34602 AN: 152014 Hom.: 4251 Cov.: 31 AF XY: 0.224 AC XY: 16629 AN XY: 74310

African (AFR) AF: 0.289 AC: 11989 AN: 41442

American (AMR) AF: 0.315 AC: 4817 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3462

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5184

South Asian (SAS) AF: 0.187 AC: 898 AN: 4808

European-Finnish (FIN) AF: 0.149 AC: 1573 AN: 10566

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13497 AN: 67958

Other (OTH) AF: 0.238 AC: 503 AN: 2116

Alfa AF: 0.206 Hom.: 417

Bravo AF: 0.243

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.68
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1590944; hg19: chr9-71636650;