rs9287675

Variant names:

• chr2-6354629-A-G
• rs9287675

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.642 AC: 26589 AN: 41422

American (AMR) AF: 0.571 AC: 8716 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3477 AN: 5174

South Asian (SAS) AF: 0.506 AC: 2432 AN: 4810

European-Finnish (FIN) AF: 0.528 AC: 5563 AN: 10534

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32850 AN: 67932

Other (OTH) AF: 0.535 AC: 1129 AN: 2112

Alfa AF: 0.504 Hom.: 80609

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
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9287675; hg19: chr2-6494761;