9-90981938-A-G

Position:

• chr9-90981938-A-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 0.98 in 152,342 control chromosomes in the GnomAD database, including 73,245 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 0.98 (73245 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90981938A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.980 AC: 149164 AN: 152224 Hom.: 73187 Cov.: 34

Gnomad AFR AF: 0.997

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.980 AC: 149281 AN: 152342 Hom.: 73245 Cov.: 34 AF XY: 0.977 AC XY: 72797 AN XY: 74492

Gnomad4 AFR AF: 0.997

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.976

Alfa AF: 0.990 Hom.: 8676

Bravo AF: 0.979

Asia WGS AF: 0.896 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs296720; hg19: chr9-93744220;