21-24305169-A-G

Variant names:

• chr21-24305169-A-G
• rs1008552
• ENST00000416218.1:n.1388T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416218.1(LINC01689):​n.1388T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,124 control chromosomes in the GnomAD database, including 59,800 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 0.86 (59800 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01689 ENST00000416218.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 2 publications found

Genes affected

LINC01689 (HGNC:52476): (long intergenic non-protein coding RNA 1689)

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416218.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01689	NR_109963.1		n.1388T>C		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01689	ENST00000416218.1	TSL:1	n.1388T>C		non_coding_transcript_exon	Exon 4 of 4
	LINC01689	ENST00000642623.1		n.517T>C		non_coding_transcript_exon	Exon 5 of 5
	LINC01684	ENST00000724112.1		n.246-1741A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.862 AC: 130994 AN: 152006 Hom.: 59772 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.899

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.862 AC: 131072 AN: 152124 Hom.: 59800 Cov.: 32 AF XY: 0.867 AC XY: 64501 AN XY: 74404

African (AFR) AF: 0.523 AC: 21687 AN: 41434

American (AMR) AF: 0.942 AC: 14373 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3437 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 0.999 AC: 4826 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10622 AN: 10622

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67856 AN: 68014

Other (OTH) AF: 0.900 AC: 1903 AN: 2114

Alfa AF: 0.901 Hom.: 8341

Bravo AF: 0.841

Asia WGS AF: 0.970 AC: 3372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1008552;

hg19: chr21-25677482;