rs9297395

Variant names:

• chr8-107503145-A-G
• rs9297395
• ENST00000657188.1:n.301-1011A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657188.1(ENSG00000286766):​n.301-1011A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,124 control chromosomes in the GnomAD database, including 7,932 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 0.28 (7932 hom., cov: 33)
• Consequence: ENSG00000286766 ENST00000657188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 4 publications found

Genes affected

ENSG00000286766 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 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
ENSG00000286766	ENST00000657188.1	n.301-1011A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42943 AN: 152006 Hom.: 7909 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.283 AC: 43013 AN: 152124 Hom.: 7932 Cov.: 33 AF XY: 0.278 AC XY: 20668 AN XY: 74388

African (AFR) AF: 0.529 AC: 21942 AN: 41468

American (AMR) AF: 0.187 AC: 2862 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3470

East Asian (EAS) AF: 0.0473 AC: 245 AN: 5184

South Asian (SAS) AF: 0.121 AC: 583 AN: 4828

European-Finnish (FIN) AF: 0.192 AC: 2038 AN: 10594

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14049 AN: 67976

Other (OTH) AF: 0.242 AC: 512 AN: 2112

Alfa AF: 0.223 Hom.: 7492

Bravo AF: 0.294

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs9297395; hg19: chr8-108515373;