rs243588

Variant names:

• chr21-17782249-T-A
• rs243588
• ENST00000430401.5:n.217-4630A>T

Your query was ambiguous. Multiple possible variants found:

• chr21-17782249-T-A
• chr21-17782249-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_007067822.1(LOC124900465):​n.2480T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LOC124900465 XR_007067822.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

Genes affected

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

LOC124900465 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900465	XR_007067822.1	n.2480T>A		non_coding_transcript_exon_variant	Exon 3 of 3
C21orf91-OT1	NR_038870.1	n.217-4630A>T		intron_variant	Intron 2 of 2
C21orf91-OT1	NR_038871.1	n.281+3299A>T		intron_variant	Intron 3 of 3
LOC124900465	XR_007067823.1	n.1605+25460T>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.217-4630A>T		intron_variant	Intron 2 of 2	1
C21orf91-OT1	ENST00000439392.1	n.281+3299A>T		intron_variant	Intron 3 of 3	1
C21orf91-OT1	ENST00000430815.5	n.230+4779A>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
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: rs243588; hg19: chr21-19154566;