chr9-118584139-T-C

Variant names:

• chr9-118584139-T-C
• rs1572299

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;