chr20-63337540-C-T

Variant names:

• chr20-63337540-C-T
• rs4603829
• ENST00000410507.1:n.*91C>T

Variant summary

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

The ENST00000410507.1(RNU6-994P):​n.*91C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,934 control chromosomes in the GnomAD database, including 24,345 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 0.56 (24345 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: RNU6-994P ENST00000410507.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

Genes affected

RNU6-994P (HGNC:47957): (RNA, U6 small nuclear 994, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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
RNU6-994P	ENST00000410507.1	n.*91C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84594 AN: 151816 Hom.: 24334 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.557 AC: 84636 AN: 151934 Hom.: 24345 Cov.: 32 AF XY: 0.558 AC XY: 41449 AN XY: 74266

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.580

Alfa AF: 0.610 Hom.: 14863

Bravo AF: 0.543

Asia WGS AF: 0.578 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4603829; hg19: chr20-61968892;