9-114818634-C-T

Variant names:

• chr9-114818634-C-T
• rs7869487

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 0.768 in 151,966 control chromosomes in the GnomAD database, including 45,792 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 0.77 (45792 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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: 0.768 AC: 116633 AN: 151846 Hom.: 45717 Cov.: 30

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.768 AC: 116773 AN: 151966 Hom.: 45792 Cov.: 30 AF XY: 0.770 AC XY: 57204 AN XY: 74288

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.746

Alfa AF: 0.754 Hom.: 5985

Bravo AF: 0.777

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7869487; hg19: chr9-117580914;