rs9287675

Variant names:

• chr2-6354629-A-G
• rs9287675

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;