rs9568867

Variant names:

• chr13-53533217-G-A
• rs9568867
• ENST00000657016.1:n.630-214219G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657016.1(ENSG00000287722):​n.630-214219G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,000 control chromosomes in the GnomAD database, including 1,741 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 0.13 (1741 hom., cov: 32)
• Consequence: ENSG00000287722 ENST00000657016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.271 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
ENSG00000287722	ENST00000657016.1	n.630-214219G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19513 AN: 151882 Hom.: 1731 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.129 AC: 19532 AN: 152000 Hom.: 1741 Cov.: 32 AF XY: 0.133 AC XY: 9859 AN XY: 74306

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.135

Alfa AF: 0.125 Hom.: 203

Bravo AF: 0.137

Asia WGS AF: 0.218 AC: 755 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9568867; hg19: chr13-54107352;