chr9-27234031-G-A

Position:

• chr9-27234031-G-A

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 0.56 in 151,826 control chromosomes in the GnomAD database, including 24,662 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 0.56 (24662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 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: 0.560 AC: 85012 AN: 151706 Hom.: 24646 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.560 AC: 85084 AN: 151826 Hom.: 24662 Cov.: 32 AF XY: 0.557 AC XY: 41293 AN XY: 74184

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.609

Alfa AF: 0.649 Hom.: 66238

Bravo AF: 0.550

Asia WGS AF: 0.597 AC: 2075 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7035592; hg19: chr9-27234029;