chr4-14693808-T-G

Variant names:

• chr4-14693808-T-G
• rs11932201
• ENST00000509654.5:n.184-121562A>C

Variant summary

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

The ENST00000509654.5(LINC00504):​n.184-121562A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,124 control chromosomes in the GnomAD database, including 4,224 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 0.23 (4224 hom., cov: 33)
• Consequence: LINC00504 ENST00000509654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 2 publications found

Genes affected

LINC00504 (HGNC:43555): (long intergenic non-protein coding RNA 504)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00504	NR_126435.1	n.224+6935A>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00504	ENST00000509654.5	n.184-121562A>C		intron_variant	Intron 2 of 4	1
LINC00504	ENST00000505089.6	n.224+6935A>C		intron_variant	Intron 3 of 6	2
LINC00504	ENST00000506292.2	n.237+6935A>C		intron_variant	Intron 3 of 3	2
LINC00504	ENST00000515031.5	n.298+6935A>C		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34742 AN: 152006 Hom.: 4205 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34806 AN: 152124 Hom.: 4224 Cov.: 33 AF XY: 0.233 AC XY: 17330 AN XY: 74370

African (AFR) AF: 0.288 AC: 11950 AN: 41464

American (AMR) AF: 0.246 AC: 3763 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1326 AN: 5176

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4824

European-Finnish (FIN) AF: 0.217 AC: 2295 AN: 10596

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12495 AN: 68012

Other (OTH) AF: 0.221 AC: 466 AN: 2108

Alfa AF: 0.205 Hom.: 6880

Bravo AF: 0.235

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.52
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11932201; hg19: chr4-14695432;