ENST00000656694.1:n.384+159C>T

Variant names:

• chr4-176893709-G-A
• rs7700025
• ENST00000656694.1:n.384+159C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656694.1(ENSG00000287544):​n.384+159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,868 control chromosomes in the GnomAD database, including 29,113 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 0.60 (29113 hom., cov: 32)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

ENSG00000287544 (HGNC:):

LINC02509 (HGNC:53498): (long intergenic non-protein coding RNA 2509)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 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
ENSG00000287544	ENST00000656694.1	n.384+159C>T		intron_variant	Intron 4 of 4
LINC02509	ENST00000670563.1	n.351+11281G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91627 AN: 151750 Hom.: 29097 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.604 AC: 91687 AN: 151868 Hom.: 29113 Cov.: 32 AF XY: 0.603 AC XY: 44768 AN XY: 74202

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.630

Alfa AF: 0.684 Hom.: 57534

Bravo AF: 0.588

Asia WGS AF: 0.586 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7700025; hg19: chr4-177814863;