rs9287675

chr2-6354629-A-G

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 0.547 in 151,936 control chromosomes in the GnomAD database, including 23,294 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 0.55 (23294 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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: 0.546 AC: 82953 AN: 151816 Hom.: 23265 Cov.: 31

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.547 AC: 83037 AN: 151936 Hom.: 23294 Cov.: 31 AF XY: 0.550 AC XY: 40851 AN XY: 74222

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.535

Alfa AF: 0.495 Hom.: 38525

Bravo AF: 0.553

Asia WGS AF: 0.557 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287675; hg19: chr2-6494761;