ENST00000416190.5:n.405-2A>G

Variant names:

• chr20-55438127-A-G
• rs212600
• ENST00000416190.5:n.405-2A>G

Variant summary

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

The ENST00000416190.5(LINC01440):​n.405-2A>G variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,162 control chromosomes in the GnomAD database, including 13,394 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 0.37 (13394 hom., cov: 33)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: LINC01440 ENST00000416190.5 splice_acceptor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.68
• Publications: 1 publications found

Genes affected

LINC01440 (HGNC:50762): (long intergenic non-protein coding RNA 1440)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01440	ENST00000416190.5	n.405-2A>G		splice_acceptor_variant, intron_variant	Intron 2 of 7	5
LINC01440	ENST00000627300.2	n.188+12057A>G		intron_variant	Intron 1 of 3	5
LINC01440	ENST00000654685.1	n.390-2A>G		splice_acceptor_variant, intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56344 AN: 152040 Hom.: 13350 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.327

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

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) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.371 AC: 56451 AN: 152156 Hom.: 13394 Cov.: 33 AF XY: 0.369 AC XY: 27427 AN XY: 74376

African (AFR) AF: 0.667 AC: 27670 AN: 41510

American (AMR) AF: 0.309 AC: 4725 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2916 AN: 5152

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4820

European-Finnish (FIN) AF: 0.193 AC: 2048 AN: 10602

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15380 AN: 67996

Other (OTH) AF: 0.330 AC: 696 AN: 2110

Alfa AF: 0.291 Hom.: 8405

Bravo AF: 0.397

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.33
PhyloP100		-5.7

Splicing

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

Other links and lift over

dbSNP: rs212600; hg19: chr20-54054665;