21-28137181-C-T

Variant names:

• chr21-28137181-C-T
• rs2831528
• ENST00000453420.5:n.706-17307G>A

Variant summary

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

The ENST00000426534.2(LINC01697):​n.1334C>T 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 0.54 in 151,930 control chromosomes in the GnomAD database, including 22,766 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 0.54 (22766 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01697 ENST00000426534.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 3 publications found

Genes affected

LINC01695 (HGNC:52483): (long intergenic non-protein coding RNA 1695)

LINC01697 (HGNC:52485): (long intergenic non-protein coding RNA 1697)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426534.2. 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
	LINC01697	NR_126010.1		n.1324C>T		non_coding_transcript_exon	Exon 5 of 5
	LINC01695	NR_126012.1		n.706-17307G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01695	ENST00000453420.5	TSL:1	n.706-17307G>A		intron	N/A
	LINC01697	ENST00000426534.2	TSL:2	n.1334C>T		non_coding_transcript_exon	Exon 5 of 5
	LINC01695	ENST00000737222.1		n.192-13327G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81918 AN: 151812 Hom.: 22719 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.508

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: 0.540 AC: 82025 AN: 151930 Hom.: 22766 Cov.: 32 AF XY: 0.536 AC XY: 39775 AN XY: 74232

African (AFR) AF: 0.662 AC: 27424 AN: 41434

American (AMR) AF: 0.568 AC: 8653 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2017 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1757 AN: 5158

South Asian (SAS) AF: 0.520 AC: 2505 AN: 4820

European-Finnish (FIN) AF: 0.434 AC: 4569 AN: 10528

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33472 AN: 67964

Other (OTH) AF: 0.512 AC: 1081 AN: 2110

Alfa AF: 0.525 Hom.: 2673

Bravo AF: 0.554

Asia WGS AF: 0.447 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.63
PhyloP100		0.10

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: rs2831528;

hg19: chr21-29509500;