chr9-87354500-T-C

Position:

• chr9-87354500-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 0.718 in 152,076 control chromosomes in the GnomAD database, including 39,775 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 0.72 (39775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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: 0.718 AC: 109059 AN: 151958 Hom.: 39726 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.718 AC: 109162 AN: 152076 Hom.: 39775 Cov.: 32 AF XY: 0.714 AC XY: 53091 AN XY: 74332

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.682

Alfa AF: 0.657 Hom.: 3383

Bravo AF: 0.706

Asia WGS AF: 0.602 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10217742; hg19: chr9-89969415;