rs1252039

Positions:

• chr9-117683256-A-T

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 0.108 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0697

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.000975

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.0946

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1252039; hg19: chr9-120445534;