9-118584139-T-C

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 0.35 in 151,816 control chromosomes in the GnomAD database, including 12,078 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 0.35 (12078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

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 (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.350 AC: 53161 AN: 151704 Hom.: 12083 Cov.: 31

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.350 AC: 53140 AN: 151816 Hom.: 12078 Cov.: 31 AF XY: 0.345 AC XY: 25587 AN XY: 74206

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.391

Alfa AF: 0.463 Hom.: 26689

Bravo AF: 0.328

Asia WGS AF: 0.131 AC: 459 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	5.9
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1572299; hg19: chr9-121346417;