rs1324165

Variant names:

• chr9-80793588-T-A
• rs1324165

Your query was ambiguous. Multiple possible variants found:

• chr9-80793588-T-A
• chr9-80793588-T-G

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 0.842 in 152,062 control chromosomes in the GnomAD database, including 54,080 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 0.84 (54080 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.842 AC: 127989 AN: 151946 Hom.: 54029 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.842 AC: 128098 AN: 152062 Hom.: 54080 Cov.: 31 AF XY: 0.848 AC XY: 63053 AN XY: 74332

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.847

Alfa AF: 0.802 Hom.: 2864

Bravo AF: 0.843

Asia WGS AF: 0.890 AC: 3097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324165; hg19: chr9-83408503;