9-90905456-A-T

Variant names:

• chr9-90905456-A-T
• rs291766

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 0.973 in 152,322 control chromosomes in the GnomAD database, including 72,104 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 0.97 (72104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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 (AMR) allele frequency at 95% confidence interval = 0.976 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: 0.973 AC: 148056 AN: 152204 Hom.: 72042 Cov.: 32

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.989

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.971

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

GnomAD4 genome AF: 0.973 AC: 148177 AN: 152322 Hom.: 72104 Cov.: 32 AF XY: 0.972 AC XY: 72428 AN XY: 74494

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.989

Gnomad4 ASJ AF: 0.982

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.986

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.971

Alfa AF: 0.974 Hom.: 9061

Bravo AF: 0.975

Asia WGS AF: 0.939 AC: 3264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs291766; hg19: chr9-93667738;