9-124119169-C-T

Variant names:

• chr9-124119169-C-T
• rs1463729

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 0.619 in 152,198 control chromosomes in the GnomAD database, including 29,720 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 0.62 (29720 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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 (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.619 AC: 94144 AN: 152080 Hom.: 29686 Cov.: 34

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.619 AC: 94226 AN: 152198 Hom.: 29720 Cov.: 34 AF XY: 0.616 AC XY: 45824 AN XY: 74410

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.606

Alfa AF: 0.575 Hom.: 50362

Bravo AF: 0.626

Asia WGS AF: 0.449 AC: 1562 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	0.40
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463729; hg19: chr9-126881448;