rs12429252

Variant names:

• chr13-30342126-A-G
• rs12429252
• ENST00000655621.1:n.171T>C

Variant summary

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

The ENST00000655621.1(LINC00426):​n.171T>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 0.138 in 152,086 control chromosomes in the GnomAD database, including 3,016 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 0.14 (3016 hom., cov: 32)
• Consequence: LINC00426 ENST00000655621.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 2 publications found

Genes affected

LINC00426 (HGNC:42761): (long intergenic non-protein coding RNA 426)

ENSG00000309792 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00426	NR_024464.2	n.406-658T>C		intron_variant	Intron 4 of 4
LOC124903145	XR_007063742.1	n.1390-2830A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00426	ENST00000655621.1	n.171T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LINC00426	ENST00000718391.1	n.473T>C		non_coding_transcript_exon_variant	Exon 5 of 6
LINC00426	ENST00000420210.6	n.271-530T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20902 AN: 151968 Hom.: 3006 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.138 AC: 20941 AN: 152086 Hom.: 3016 Cov.: 32 AF XY: 0.141 AC XY: 10447 AN XY: 74350

African (AFR) AF: 0.306 AC: 12690 AN: 41426

American (AMR) AF: 0.222 AC: 3395 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2307 AN: 5174

South Asian (SAS) AF: 0.0833 AC: 401 AN: 4816

European-Finnish (FIN) AF: 0.0152 AC: 161 AN: 10604

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0242 AC: 1646 AN: 68002

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.0781 Hom.: 387

Bravo AF: 0.170

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12429252; hg19: chr13-30916263;