rs914238

Variant names:

• chr21-45595747-T-C
• rs914238
• ENST00000820224.1:n.1373A>G

Variant summary

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

The ENST00000820224.1(ENSG00000286082):​n.1373A>G 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 0.476 in 152,286 control chromosomes in the GnomAD database, including 17,320 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 (17299 hom., cov: 34)
  • Exomes 𝑓: 0.50 (21 hom.)
• Consequence: ENSG00000286082 ENST00000820224.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 6 publications found

Genes affected

ENSG00000286082 (HGNC:):

LINC01694 (HGNC:52481): (long intergenic non-protein coding RNA 1694)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820224.1. 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
	LINC01694	NR_146912.1		n.56-644T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286082	ENST00000820224.1		n.1373A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286082	ENST00000820225.1		n.1474A>G		non_coding_transcript_exon	Exon 2 of 2
	LINC01694	ENST00000424569.2	TSL:5	n.144+86T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72276 AN: 152020 Hom.: 17274 Cov.: 34

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.500 AC: 75 AN: 150 Hom.: 21 AF XY: 0.480 AC XY: 47 AN XY: 98

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.444 AC: 16 AN: 36

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.533 AC: 48 AN: 90

Other (OTH) AF: 0.500 AC: 8 AN: 16

GnomAD4 genome AF: 0.476 AC: 72349 AN: 152136 Hom.: 17299 Cov.: 34 AF XY: 0.478 AC XY: 35583 AN XY: 74374

African (AFR) AF: 0.454 AC: 18837 AN: 41512

American (AMR) AF: 0.466 AC: 7121 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2294 AN: 5174

South Asian (SAS) AF: 0.577 AC: 2784 AN: 4824

European-Finnish (FIN) AF: 0.479 AC: 5069 AN: 10578

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32999 AN: 67972

Other (OTH) AF: 0.491 AC: 1035 AN: 2110

Alfa AF: 0.484 Hom.: 68095

Bravo AF: 0.469

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.34
PhyloP100		0.61

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: rs914238;

hg19: chr21-47015661;