9-97887977-A-T

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 0.498 in 151,924 control chromosomes in the GnomAD database, including 20,271 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 0.50 (20271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.498 AC: 75601 AN: 151806 Hom.: 20232 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.498 AC: 75684 AN: 151924 Hom.: 20271 Cov.: 31 AF XY: 0.505 AC XY: 37513 AN XY: 74258

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.464

Alfa AF: 0.447 Hom.: 2021

Bravo AF: 0.509

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	14
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: rs7853349; hg19: chr9-100650259;