9-80980146-G-A

Position:

• chr9-80980146-G-A

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 0.566 in 151,956 control chromosomes in the GnomAD database, including 25,762 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 0.57 (25762 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85866 AN: 151838 Hom.: 25736 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.566 AC: 85952 AN: 151956 Hom.: 25762 Cov.: 33 AF XY: 0.568 AC XY: 42152 AN XY: 74232

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.575

Alfa AF: 0.502 Hom.: 4706

Bravo AF: 0.583

Asia WGS AF: 0.686 AC: 2381 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13285452; hg19: chr9-83595061;