20-4489235-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000238282 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419863.1. 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
	ENSG00000238282	ENST00000419863.1	TSL:5	n.41+13557C>T		intron	N/A

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

African (AFR) AF: 0.0262 AC: 1088 AN: 41536

American (AMR) AF: 0.150 AC: 2294 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.578 AC: 2976 AN: 5148

South Asian (SAS) AF: 0.323 AC: 1553 AN: 4814

European-Finnish (FIN) AF: 0.133 AC: 1405 AN: 10578

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8169 AN: 67974

Other (OTH) AF: 0.131 AC: 276 AN: 2114

Alfa AF: 0.118 Hom.: 2080

Bravo AF: 0.118

Asia WGS AF: 0.419 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		0.27

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: rs6133127;

hg19: chr20-4469883;