21-21776930-A-G

Variant names:

• chr21-21776930-A-G
• rs8131512
• ENST00000430060.1:n.350-8043A>G

Variant summary

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

The ENST00000430060.1(LINC01425):​n.350-8043A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,420 control chromosomes in the GnomAD database, including 3,248 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 0.16 (3248 hom., cov: 31)
• Consequence: LINC01425 ENST00000430060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 1 publications found

Genes affected

LINC01425 (HGNC:50733): (long intergenic non-protein coding RNA 1425)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430060.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01425	NR_109958.1		n.350-8043A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01425	ENST00000430060.1	TSL:1	n.350-8043A>G		intron	N/A
	LINC01425	ENST00000425979.6	TSL:2	n.117-8043A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23883 AN: 151306 Hom.: 3221 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0833

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.158 AC: 23947 AN: 151420 Hom.: 3248 Cov.: 31 AF XY: 0.153 AC XY: 11303 AN XY: 73982

African (AFR) AF: 0.364 AC: 14951 AN: 41098

American (AMR) AF: 0.0978 AC: 1489 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0987 AC: 342 AN: 3464

East Asian (EAS) AF: 0.0574 AC: 295 AN: 5140

South Asian (SAS) AF: 0.0506 AC: 242 AN: 4786

European-Finnish (FIN) AF: 0.0541 AC: 567 AN: 10480

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0833 AC: 5660 AN: 67920

Other (OTH) AF: 0.151 AC: 318 AN: 2104

Alfa AF: 0.116 Hom.: 2074

Bravo AF: 0.171

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.40
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs8131512; hg19: chr21-23149250;