chr9-27599748-T-C

Position:

• chr9-27599748-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.47 (5317 hom., cov: 13)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 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: 0.466 AC: 35637 AN: 76502 Hom.: 5311 Cov.: 13

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.466 AC: 35656 AN: 76544 Hom.: 5317 Cov.: 13 AF XY: 0.466 AC XY: 16524 AN XY: 35452

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.474

Alfa AF: 0.300 Hom.: 9861

Asia WGS AF: 0.223 AC: 750 AN: 3374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2477518; hg19: chr9-27599746;