chr13-63455577-C-G

Position:

• chr13-63455577-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287996 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903236	XR_007063922.1	n.416-55910C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287996	ENST00000652818.1	n.416-55910C>G		intron_variant
ENSG00000287996	ENST00000656278.1	n.383-3350C>G		intron_variant
ENSG00000287996	ENST00000666997.1	n.513-3350C>G		intron_variant

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

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.210

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9564057; hg19: chr13-64029710;