13-21877232-T-C

Variant names:

• chr13-21877232-T-C
• rs765244
• ENST00000413124.4:n.128+903A>G

Variant summary

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

The ENST00000624644.2(LINC00424):​n.122+903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,066 control chromosomes in the GnomAD database, including 4,829 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 0.25 (4829 hom., cov: 32)
• Consequence: LINC00424 ENST00000624644.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 4 publications found

Genes affected

LINC00424 (HGNC:42815): (long intergenic non-protein coding RNA 424)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624644.2. 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
	LINC00424	NR_047040.1		n.26+903A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00424	ENST00000413124.4	TSL:4	n.128+903A>G		intron	N/A
	LINC00424	ENST00000624644.2	TSL:3	n.122+903A>G		intron	N/A
	LINC00424	ENST00000669854.1		n.122+903A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37913 AN: 151946 Hom.: 4829 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.249 AC: 37929 AN: 152066 Hom.: 4829 Cov.: 32 AF XY: 0.246 AC XY: 18276 AN XY: 74314

African (AFR) AF: 0.206 AC: 8543 AN: 41476

American (AMR) AF: 0.229 AC: 3494 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5168

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4818

European-Finnish (FIN) AF: 0.228 AC: 2407 AN: 10566

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18986 AN: 67970

Other (OTH) AF: 0.250 AC: 525 AN: 2104

Alfa AF: 0.271 Hom.: 25023

Bravo AF: 0.249

Asia WGS AF: 0.267 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.23
PhyloP100		0.036

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: rs765244;

hg19: chr13-22451371;