ENST00000414161.1:n.113+242A>G

Variant names:

• chr13-38544945-T-C
• rs2323883
• ENST00000414161.1:n.113+242A>G

Variant summary

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

The ENST00000414161.1(LINC00437):​n.113+242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,082 control chromosomes in the GnomAD database, including 40,292 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 0.70 (40292 hom., cov: 32)
• Consequence: LINC00437 ENST00000414161.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 5 publications found

Genes affected

LINC00437 (HGNC:42772): (long intergenic non-protein coding RNA 437)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00437	NR_126377.1	n.339-10925A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00437	ENST00000414161.1	n.113+242A>G		intron_variant	Intron 1 of 1	1
LINC00437	ENST00000756067.1	n.588-10925A>G		intron_variant	Intron 2 of 2
LINC00437	ENST00000756068.1	n.487-10925A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106097 AN: 151964 Hom.: 40300 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.698 AC: 106103 AN: 152082 Hom.: 40292 Cov.: 32 AF XY: 0.702 AC XY: 52171 AN XY: 74358

African (AFR) AF: 0.373 AC: 15446 AN: 41440

American (AMR) AF: 0.758 AC: 11583 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2558 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3735 AN: 5146

South Asian (SAS) AF: 0.669 AC: 3225 AN: 4824

European-Finnish (FIN) AF: 0.930 AC: 9863 AN: 10604

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57266 AN: 68010

Other (OTH) AF: 0.689 AC: 1452 AN: 2108

Alfa AF: 0.804 Hom.: 142516

Bravo AF: 0.672

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2323883; hg19: chr13-39119082;