ENST00000657016.1:n.629+186724G>A

Variant names:

• chr13-53490846-G-A
• rs9568856
• ENST00000657016.1:n.629+186724G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000657016.1(ENSG00000287722):​n.629+186724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,818 control chromosomes in the GnomAD database, including 4,421 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 0.22 (4421 hom., cov: 32)
• Consequence: ENSG00000287722 ENST00000657016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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.629+186724G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33009 AN: 151698 Hom.: 4409 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.218 AC: 33066 AN: 151818 Hom.: 4421 Cov.: 32 AF XY: 0.220 AC XY: 16321 AN XY: 74246

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.192

Alfa AF: 0.142 Hom.: 3399

Bravo AF: 0.240

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	14
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9568856; hg19: chr13-54064981;