20-4488442-C-T

Variant names:

• chr20-4488442-C-T
• rs6139438
• ENST00000419863.1:n.41+12764C>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+12764C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,172 control chromosomes in the GnomAD database, including 2,017 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 (2017 hom., cov: 32)
• Consequence: ENSG00000238282 ENST00000419863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 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+12764C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18312 AN: 152054 Hom.: 2025 Cov.: 32

Gnomad AFR AF: 0.0262

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.120 AC: 18292 AN: 152172 Hom.: 2017 Cov.: 32 AF XY: 0.126 AC XY: 9359 AN XY: 74386

African (AFR) AF: 0.0261 AC: 1083 AN: 41536

American (AMR) AF: 0.150 AC: 2285 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 278 AN: 3468

East Asian (EAS) AF: 0.576 AC: 2971 AN: 5158

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4822

European-Finnish (FIN) AF: 0.133 AC: 1409 AN: 10582

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

European-Non Finnish (NFE) AF: 0.120 AC: 8152 AN: 68008

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.112 Hom.: 145

Bravo AF: 0.118

Asia WGS AF: 0.415 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6139438; hg19: chr20-4469090;