rs1012203

Variant names:

• chr9-101864426-A-G
• rs1012203

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 0.0914 in 152,178 control chromosomes in the GnomAD database, including 703 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 0.091 (703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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: 0.0914 AC: 13900 AN: 152060 Hom.: 702 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0968

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0914 AC: 13916 AN: 152178 Hom.: 703 Cov.: 32 AF XY: 0.0926 AC XY: 6885 AN XY: 74380

Gnomad4 AFR AF: 0.0658

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0955 Hom.: 1007

Bravo AF: 0.0893

Asia WGS AF: 0.150 AC: 521 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.34
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012203; hg19: chr9-104626708;