9-27581241-T-C

Position:

• chr9-27581241-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.482 in 151,802 control chromosomes in the GnomAD database, including 17,748 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 0.48 (17748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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: 0.482 AC: 73144 AN: 151682 Hom.: 17726 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.482 AC: 73211 AN: 151802 Hom.: 17748 Cov.: 33 AF XY: 0.482 AC XY: 35736 AN XY: 74210

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.483

Alfa AF: 0.477 Hom.: 17658

Bravo AF: 0.490

Asia WGS AF: 0.469 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	11
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2783010; hg19: chr9-27581239;