rs1252039

Variant names:

• chr9-117683256-A-T
• rs1252039

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 0.108 in 151,734 control chromosomes in the GnomAD database, including 1,129 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 0.11 (1129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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: 0.108 AC: 16433 AN: 151616 Hom.: 1131 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.000972

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0778

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.108 AC: 16447 AN: 151734 Hom.: 1129 Cov.: 32 AF XY: 0.109 AC XY: 8103 AN XY: 74134

African (AFR) AF: 0.193 AC: 7995 AN: 41412

American (AMR) AF: 0.0697 AC: 1059 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3466

East Asian (EAS) AF: 0.000975 AC: 5 AN: 5130

South Asian (SAS) AF: 0.119 AC: 573 AN: 4828

European-Finnish (FIN) AF: 0.100 AC: 1061 AN: 10570

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0777 AC: 5272 AN: 67824

Other (OTH) AF: 0.0946 AC: 199 AN: 2104

Alfa AF: 0.0933 Hom.: 89

Bravo AF: 0.106

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.4
DANN	Benign	0.60
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs1252039; hg19: chr9-120445534;