9-124119169-C-T

Position:

• chr9-124119169-C-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 0.619 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;