chr20-5423880-G-C

Variant names:

• chr20-5423880-G-C
• rs4815812
• ENST00000668553.1:n.1280+17483G>C

Variant summary

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

The ENST00000668553.1(ENSG00000266908):​n.1280+17483G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,136 control chromosomes in the GnomAD database, including 50,694 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 0.81 (50694 hom., cov: 30)
• Consequence: ENSG00000266908 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

Genes affected

ENSG00000266908 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 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
ENSG00000266908	ENST00000668553.1	n.1280+17483G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123544 AN: 152018 Hom.: 50641 Cov.: 30

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.813 AC: 123652 AN: 152136 Hom.: 50694 Cov.: 30 AF XY: 0.821 AC XY: 61076 AN XY: 74366

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.800

Alfa AF: 0.703 Hom.: 2032

Bravo AF: 0.817

Asia WGS AF: 0.894 AC: 3107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815812; hg19: chr20-5404526;