chr21-24538446-C-A

Position:

• chr21-24538446-C-A

Variant summary

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

The NR_135519.1(LINC01684):​n.270-7549C>A 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 0.136 in 152,040 control chromosomes in the GnomAD database, including 1,676 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 0.14 (1676 hom., cov: 32)
• Consequence: LINC01684 NR_135519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

LINC01684 (HGNC:52472): (long intergenic non-protein coding RNA 1684)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01684	NR_135519.1	n.270-7549C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01684	ENST00000415182.1	n.229-7549C>A		intron_variant, non_coding_transcript_variant		1
LINC01684	ENST00000655039.1	n.168-7549C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20638 AN: 151922 Hom.: 1674 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0561

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.136 AC: 20676 AN: 152040 Hom.: 1676 Cov.: 32 AF XY: 0.136 AC XY: 10128 AN XY: 74298

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0828

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.0924

Gnomad4 OTH AF: 0.123

Alfa AF: 0.108 Hom.: 494

Bravo AF: 0.138

Asia WGS AF: 0.102 AC: 355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2829156; hg19: chr21-25910760;