21-17787449-G-A

Variant names:

• chr21-17787449-G-A
• rs243601
• ENST00000430401.5:n.34-239C>T

Variant summary

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

The ENST00000430401.5(C21orf91-OT1):​n.34-239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,762 control chromosomes in the GnomAD database, including 19,406 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 0.50 (19406 hom., cov: 31)
• Consequence: C21orf91-OT1 ENST00000430401.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C21orf91-OT1	NR_038870.1	n.34-239C>T		intron_variant	Intron 1 of 2
C21orf91-OT1	NR_038871.1	n.34-239C>T		intron_variant	Intron 1 of 3
LOC124900465	XR_007067823.1	n.1605+30660G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C21orf91-OT1	ENST00000430401.5	n.34-239C>T		intron_variant	Intron 1 of 2	1
C21orf91-OT1	ENST00000439392.1	n.34-239C>T		intron_variant	Intron 1 of 3	1
C21orf91-OT1	ENST00000430815.5	n.48-239C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76519 AN: 151644 Hom.: 19384 Cov.: 31

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.505 AC: 76591 AN: 151762 Hom.: 19406 Cov.: 31 AF XY: 0.507 AC XY: 37574 AN XY: 74144

African (AFR) AF: 0.542 AC: 22407 AN: 41360

American (AMR) AF: 0.480 AC: 7312 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1756 AN: 3466

East Asian (EAS) AF: 0.516 AC: 2662 AN: 5162

South Asian (SAS) AF: 0.566 AC: 2724 AN: 4812

European-Finnish (FIN) AF: 0.501 AC: 5268 AN: 10522

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32662 AN: 67898

Other (OTH) AF: 0.526 AC: 1110 AN: 2110

Alfa AF: 0.384 Hom.: 1283

Bravo AF: 0.503

Asia WGS AF: 0.531 AC: 1846 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	7.3
DANN	Benign	0.63
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs243601; hg19: chr21-19159766;