20-4488282-G-C

Position:

• chr20-4488282-G-C

Variant summary

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

The ENST00000419863.1(ENSG00000238282):​n.41+12604G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,066 control chromosomes in the GnomAD database, including 2,931 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 0.17 (2931 hom., cov: 32)
• Consequence: ENST00000419863.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000419863.1	n.41+12604G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26401 AN: 151948 Hom.: 2935 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.174 AC: 26408 AN: 152066 Hom.: 2931 Cov.: 32 AF XY: 0.177 AC XY: 13145 AN XY: 74320

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0891

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0687 Hom.: 82

Bravo AF: 0.178

Asia WGS AF: 0.428 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6139437; hg19: chr20-4468930;