rs565453

Variant names:

• chr5-112849696-A-C
• rs565453
• ENST00000520401.1:n.229-6953A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-112849696-A-C
• chr5-112849696-A-G
• chr5-112849696-A-T

Variant summary

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

The ENST00000520401.1(ENSG00000258864):​n.229-6953A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,004 control chromosomes in the GnomAD database, including 32,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars).

• Frequency: Genomes: 𝑓 0.65 (32036 hom., cov: 31)
• Consequence: ENSG00000258864 ENST00000520401.1 intron
• Clinical Significance: other no assertion criteria provided O:1
• Conservation: PhyloP100: 0.00

Genes affected

ENSG00000258864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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
ENSG00000258864	ENST00000520401.1	n.229-6953A>C		intron_variant	Intron 3 of 7	3		ENSP00000454861.1

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98263 AN: 151886 Hom.: 32019 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.647 AC: 98332 AN: 152004 Hom.: 32036 Cov.: 31 AF XY: 0.648 AC XY: 48166 AN XY: 74304

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.656

Alfa AF: 0.582 Hom.: 2907

Bravo AF: 0.656

Asia WGS AF: 0.764 AC: 2655 AN: 3478

ClinVar

Significance: other

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Familial colorectal cancer Other:1

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Systems Biology Platform Zhejiang California International NanoSystems Institute

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs565453; hg19: chr5-112185393;