21-17787983-T-C

Variant summary

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

The NR_038870.1(C21orf91-OT1):n.34-773A>G 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 0.479 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 NR_038870.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22

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=-0.87).
• 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/exons	MANE	UniProt
C21orf91-OT1	NR_038870.1	n.34-773A>G		intron_variant, non_coding_transcript_variant
LOC124900465	XR_007067823.1	n.1605+31194T>C		intron_variant, non_coding_transcript_variant
C21orf91-OT1	NR_038871.1	n.34-773A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C21orf91-OT1	ENST00000430401.5	n.34-773A>G		intron_variant, non_coding_transcript_variant		1
C21orf91-OT1	ENST00000430815.5	n.48-773A>G		intron_variant, non_coding_transcript_variant		5
C21orf91-OT1	ENST00000439392.1	n.34-773A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.506

Alfa AF: 0.460 Hom.: 1999

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243603; hg19: chr21-19160300;