ENST00000430401.5:n.34-773A>G

Variant names:

• chr21-17787983-T-C
• rs243603
• ENST00000430401.5:n.34-773A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430401.5(C21orf91-OT1):​n.34-773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,930 control chromosomes in the GnomAD database, including 17,533 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 0.48 (17533 hom., cov: 32)
• Consequence: C21orf91-OT1 ENST00000430401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22
• Publications: 4 publications found

Genes affected

C21orf91-OT1 (HGNC:16729): (C21orf91 overlapping transcript 1)

ENSG00000244676 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C21orf91-OT1	NR_038870.1	n.34-773A>G		intron_variant	Intron 1 of 2
C21orf91-OT1	NR_038871.1	n.34-773A>G		intron_variant	Intron 1 of 3
LOC124900465	XR_007067823.1	n.1605+31194T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C21orf91-OT1	ENST00000430401.5	n.34-773A>G		intron_variant	Intron 1 of 2	1
C21orf91-OT1	ENST00000439392.1	n.34-773A>G		intron_variant	Intron 1 of 3	1
C21orf91-OT1	ENST00000430815.5	n.48-773A>G		intron_variant	Intron 1 of 4	5
ENSG00000244676	ENST00000813924.1	n.192-22512T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72781 AN: 151814 Hom.: 17514 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.479 AC: 72849 AN: 151930 Hom.: 17533 Cov.: 32 AF XY: 0.482 AC XY: 35777 AN XY: 74276

African (AFR) AF: 0.468 AC: 19380 AN: 41428

American (AMR) AF: 0.470 AC: 7174 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1757 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2651 AN: 5160

South Asian (SAS) AF: 0.555 AC: 2664 AN: 4802

European-Finnish (FIN) AF: 0.482 AC: 5084 AN: 10546

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32388 AN: 67956

Other (OTH) AF: 0.506 AC: 1064 AN: 2104

Alfa AF: 0.460 Hom.: 2082

Bravo AF: 0.477

Asia WGS AF: 0.523 AC: 1809 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.8
DANN	Benign	0.45
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs243603; hg19: chr21-19160300;