chr4-14695868-G-A

Variant names:

• chr4-14695868-G-A
• rs11728802
• ENST00000509654.5:n.184-123622C>T

Variant summary

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

The ENST00000509654.5(LINC00504):​n.184-123622C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,838 control chromosomes in the GnomAD database, including 17,974 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 0.47 (17974 hom., cov: 32)
• Consequence: LINC00504 ENST00000509654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00504	NR_126435.1	n.224+4875C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00504	ENST00000509654.5	n.184-123622C>T		intron_variant	Intron 2 of 4	1
LINC00504	ENST00000505089.6	n.224+4875C>T		intron_variant	Intron 3 of 6	2
LINC00504	ENST00000506292.2	n.237+4875C>T		intron_variant	Intron 3 of 3	2
LINC00504	ENST00000515031.5	n.298+4875C>T		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71756 AN: 151720 Hom.: 17963 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.473 AC: 71771 AN: 151838 Hom.: 17974 Cov.: 32 AF XY: 0.473 AC XY: 35118 AN XY: 74220

African (AFR) AF: 0.300 AC: 12431 AN: 41392

American (AMR) AF: 0.529 AC: 8076 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2160 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2303 AN: 5148

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4814

European-Finnish (FIN) AF: 0.510 AC: 5366 AN: 10524

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37369 AN: 67914

Other (OTH) AF: 0.494 AC: 1042 AN: 2110

Alfa AF: 0.469 Hom.: 2472

Bravo AF: 0.466

Asia WGS AF: 0.429 AC: 1490 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.45
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11728802; hg19: chr4-14697492;