rs243605

Positions:

• chr21-17788803-G-C
• chr21-17788803-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.34-1593C>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 0.481 in 151,706 control chromosomes in the GnomAD database, including 17,580 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 (17580 hom., cov: 30)
• Consequence: C21orf91-OT1 NR_038870.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

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=-0.84).
• 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	Protein	UniProt
C21orf91-OT1	NR_038870.1	n.34-1593C>G		intron_variant, non_coding_transcript_variant
LOC124900465	XR_007067823.1	n.1605+32014G>C		intron_variant, non_coding_transcript_variant
C21orf91-OT1	NR_038871.1	n.34-1593C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C21orf91-OT1	ENST00000430401.5	n.34-1593C>G		intron_variant, non_coding_transcript_variant		1
C21orf91-OT1	ENST00000430815.5	n.48-1593C>G		intron_variant, non_coding_transcript_variant		5
C21orf91-OT1	ENST00000439392.1	n.34-1593C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72850 AN: 151588 Hom.: 17560 Cov.: 30

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.481 AC: 72920 AN: 151706 Hom.: 17580 Cov.: 30 AF XY: 0.483 AC XY: 35793 AN XY: 74118

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.506

Alfa AF: 0.301 Hom.: 688

Bravo AF: 0.478

Asia WGS AF: 0.522 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.5
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: rs243605; hg19: chr21-19161120;