rs1013324

Positions:

• chr9-120249410-A-G
• chr9-120249410-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 0.712 in 152,062 control chromosomes in the GnomAD database, including 42,268 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 0.71 (42268 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.713 AC: 108293 AN: 151944 Hom.: 42259 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.712 AC: 108334 AN: 152062 Hom.: 42268 Cov.: 31 AF XY: 0.719 AC XY: 53419 AN XY: 74340

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.759

Alfa AF: 0.716 Hom.: 6044

Bravo AF: 0.695

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013324; hg19: chr9-123011688;