ENST00000510907.5:n.281+76417A>G

Variant names:

• chr4-13734271-A-G
• rs7688193
• ENST00000510907.5:n.281+76417A>G

Variant summary

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

The ENST00000510907.5(LINC01182):​n.281+76417A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,244 control chromosomes in the GnomAD database, including 5,060 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 0.24 (5060 hom., cov: 33)
• Consequence: LINC01182 ENST00000510907.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 1 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01182	NR_121681.1	n.281+76417A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000510907.5	n.281+76417A>G		intron_variant	Intron 2 of 3	2
LINC01182	ENST00000669061.1	n.548+76417A>G		intron_variant	Intron 2 of 4
LINC01182	ENST00000715489.1	n.281+76417A>G		intron_variant	Intron 2 of 8
LINC01182	ENST00000816953.1	n.268+76417A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35994 AN: 152126 Hom.: 5060 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.236 AC: 35987 AN: 152244 Hom.: 5060 Cov.: 33 AF XY: 0.234 AC XY: 17421 AN XY: 74442

African (AFR) AF: 0.100 AC: 4154 AN: 41560

American (AMR) AF: 0.234 AC: 3574 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3472

East Asian (EAS) AF: 0.0443 AC: 230 AN: 5194

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4820

European-Finnish (FIN) AF: 0.250 AC: 2654 AN: 10606

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22199 AN: 67998

Other (OTH) AF: 0.233 AC: 492 AN: 2116

Alfa AF: 0.293 Hom.: 22310

Bravo AF: 0.225

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.50
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7688193; hg19: chr4-13735895;