9-134245399-T-C

Position:

• chr9-134245399-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 0.735 in 152,202 control chromosomes in the GnomAD database, including 41,327 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 0.74 (41327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.798 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: 0.735 AC: 111816 AN: 152084 Hom.: 41290 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.735 AC: 111911 AN: 152202 Hom.: 41327 Cov.: 33 AF XY: 0.740 AC XY: 55040 AN XY: 74400

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.741

Alfa AF: 0.707 Hom.: 56433

Bravo AF: 0.745

Asia WGS AF: 0.765 AC: 2663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917360; hg19: chr9-137137245;