9-90981938-A-G

Variant names:

• chr9-90981938-A-G
• rs296720

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;