9-73794510-A-G

Variant names:

• chr9-73794510-A-G
• rs1379911

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 0.877 in 151,360 control chromosomes in the GnomAD database, including 59,002 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 0.88 (59002 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 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: 0.877 AC: 132606 AN: 151244 Hom.: 58978 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.942

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.877 AC: 132682 AN: 151360 Hom.: 59002 Cov.: 30 AF XY: 0.878 AC XY: 64922 AN XY: 73954

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.899

Alfa AF: 0.913 Hom.: 7500

Bravo AF: 0.862

Asia WGS AF: 0.873 AC: 2995 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1379911; hg19: chr9-76409426;