chr13-53525714-C-A

Variant names:

• chr13-53525714-C-A
• rs9316628
• ENST00000657016.1:n.629+221592C>A

Variant summary

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

The ENST00000657016.1(ENSG00000287722):​n.629+221592C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,920 control chromosomes in the GnomAD database, including 5,411 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 0.26 (5411 hom., cov: 32)
• Consequence: ENSG00000287722 ENST00000657016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

Genes affected

ENSG00000287722 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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+221592C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39888 AN: 151802 Hom.: 5403 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.263 AC: 39911 AN: 151920 Hom.: 5411 Cov.: 32 AF XY: 0.262 AC XY: 19429 AN XY: 74238

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.243

Alfa AF: 0.282 Hom.: 12485

Bravo AF: 0.253

Asia WGS AF: 0.214 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9316628; hg19: chr13-54099849; COSMIC: COSV69350329;