chr21-17787449-G-A

Position:

• chr21-17787449-G-A

Variant summary

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

The NR_038870.1(C21orf91-OT1):​n.34-239C>T 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 0.505 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 NR_038870.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622

Genes affected

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

LOC124900465 (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 (SAS) 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
C21orf91-OT1	NR_038870.1	n.34-239C>T		intron_variant, non_coding_transcript_variant
LOC124900465	XR_007067823.1	n.1605+30660G>A		intron_variant, non_coding_transcript_variant
C21orf91-OT1	NR_038871.1	n.34-239C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C21orf91-OT1	ENST00000430401.5	n.34-239C>T		intron_variant, non_coding_transcript_variant		1
C21orf91-OT1	ENST00000430815.5	n.48-239C>T		intron_variant, non_coding_transcript_variant		5
C21orf91-OT1	ENST00000439392.1	n.34-239C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.526

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243601; hg19: chr21-19159766;