20-4489235-C-T

Variant names:

• chr20-4489235-C-T
• rs6133127
• ENST00000419863.1:n.41+13557C>T

Variant summary

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

The ENST00000419863.1(ENSG00000238282):​n.41+13557C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,128 control chromosomes in the GnomAD database, including 2,035 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 0.12 (2035 hom., cov: 32)
• Consequence: ENSG00000238282 ENST00000419863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

ENSG00000238282 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 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
ENSG00000238282	ENST00000419863.1	n.41+13557C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18369 AN: 152010 Hom.: 2043 Cov.: 32

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.121 AC: 18349 AN: 152128 Hom.: 2035 Cov.: 32 AF XY: 0.126 AC XY: 9371 AN XY: 74364

Gnomad4 AFR AF: 0.0262

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.131

Alfa AF: 0.120 Hom.: 1727

Bravo AF: 0.118

Asia WGS AF: 0.419 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6133127; hg19: chr20-4469883;