rs9568867

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287722	ENST00000657016.1		n.630-214219G>A		intron	N/A
	ENSG00000288768	ENST00000748651.1		n.379-25030G>A		intron	N/A

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

African (AFR) AF: 0.0449 AC: 1859 AN: 41426

American (AMR) AF: 0.278 AC: 4242 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5162

South Asian (SAS) AF: 0.186 AC: 896 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1457 AN: 10558

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.128 AC: 8671 AN: 67976

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.127 Hom.: 2055

Bravo AF: 0.137

Asia WGS AF: 0.218 AC: 755 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.53
PhyloP100		0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9568867;

hg19: chr13-54107352;