rs9287293

Variant names:

• chr1-13882076-G-A
• rs9287293

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 0.0934 in 152,144 control chromosomes in the GnomAD database, including 949 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 0.093 (949 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 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: 0.0933 AC: 14188 AN: 152026 Hom.: 944 Cov.: 33

Gnomad AFR AF: 0.0615

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.0872

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.0934 AC: 14205 AN: 152144 Hom.: 949 Cov.: 33 AF XY: 0.0968 AC XY: 7197 AN XY: 74366

African (AFR) AF: 0.0617 AC: 2561 AN: 41524

American (AMR) AF: 0.0952 AC: 1456 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0872 AC: 302 AN: 3464

East Asian (EAS) AF: 0.383 AC: 1986 AN: 5180

South Asian (SAS) AF: 0.105 AC: 506 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1300 AN: 10552

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0849 AC: 5775 AN: 68004

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0890 Hom.: 2236

Bravo AF: 0.0929

Asia WGS AF: 0.226 AC: 782 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.39
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs9287293; hg19: chr1-14208571;