13-63455577-C-G

Variant names:

• chr13-63455577-C-G
• rs9564057
• ENST00000652818.1:n.416-55910C>G

Variant summary

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

The ENST00000652818.1(ENSG00000287996):​n.416-55910C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,958 control chromosomes in the GnomAD database, including 2,711 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 0.17 (2711 hom., cov: 32)
• Consequence: ENSG00000287996 ENST00000652818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 0 publications found

Genes affected

ENSG00000287996 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652818.1. 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
	ENSG00000287996	ENST00000652818.1		n.416-55910C>G		intron	N/A
	ENSG00000287996	ENST00000656278.1		n.383-3350C>G		intron	N/A
	ENSG00000287996	ENST00000666997.1		n.513-3350C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25838 AN: 151840 Hom.: 2708 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.170 AC: 25841 AN: 151958 Hom.: 2711 Cov.: 32 AF XY: 0.168 AC XY: 12471 AN XY: 74276

African (AFR) AF: 0.0539 AC: 2234 AN: 41484

American (AMR) AF: 0.234 AC: 3569 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3466

East Asian (EAS) AF: 0.106 AC: 546 AN: 5162

South Asian (SAS) AF: 0.107 AC: 518 AN: 4822

European-Finnish (FIN) AF: 0.215 AC: 2258 AN: 10524

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14726 AN: 67934

Other (OTH) AF: 0.210 AC: 442 AN: 2106

Alfa AF: 0.0933 Hom.: 148

Bravo AF: 0.169

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.38
PhyloP100		-1.9

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: rs9564057;

hg19: chr13-64029710;