9-26281341-G-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 0.58 in 151,910 control chromosomes in the GnomAD database, including 26,455 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 0.58 (26455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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: 0.580 AC: 88060 AN: 151792 Hom.: 26415 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.580 AC: 88151 AN: 151910 Hom.: 26455 Cov.: 32 AF XY: 0.584 AC XY: 43317 AN XY: 74224

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.563

Alfa AF: 0.428 Hom.: 1220

Bravo AF: 0.592

Asia WGS AF: 0.796 AC: 2763 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.0070
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs375658; hg19: chr9-26281339; COSMIC: COSV60346643;