rs1013324

Variant names:

• chr9-120249410-A-G
• rs1013324

Your query was ambiguous. Multiple possible variants found:

• chr9-120249410-A-G
• chr9-120249410-A-T

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 0.712 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.360 AC: 14910 AN: 41414

American (AMR) AF: 0.812 AC: 12423 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.934 AC: 4834 AN: 5176

South Asian (SAS) AF: 0.892 AC: 4292 AN: 4812

European-Finnish (FIN) AF: 0.845 AC: 8945 AN: 10586

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57382 AN: 67996

Other (OTH) AF: 0.759 AC: 1602 AN: 2110

Alfa AF: 0.704 Hom.: 6103

Bravo AF: 0.695

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.66
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs1013324; hg19: chr9-123011688;