9-88208691-T-A

Position:

• chr9-88208691-T-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 0.588 in 152,094 control chromosomes in the GnomAD database, including 30,306 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 0.59 (30306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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 = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89415 AN: 151976 Hom.: 30298 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.588 AC: 89435 AN: 152094 Hom.: 30306 Cov.: 32 AF XY: 0.591 AC XY: 43916 AN XY: 74338

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.657

Alfa AF: 0.657 Hom.: 4424

Bravo AF: 0.560

Asia WGS AF: 0.535 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251622; hg19: chr9-90823606;