rs11728802

chr4-14695868-G-Achr4-14695868-G-T

Variant summary

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

The NR_126435.1(LINC00504):n.224+4875C>T variant causes a intron, non coding transcript 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 NR_126435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00504	NR_126435.1	n.224+4875C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00504	ENST00000505089.6	n.224+4875C>T		intron_variant, non_coding_transcript_variant		2
LINC00504	ENST00000509654.5	n.184-123622C>T		intron_variant, non_coding_transcript_variant		1
LINC00504	ENST00000506292.2	n.237+4875C>T		intron_variant, non_coding_transcript_variant		2
LINC00504	ENST00000515031.5	n.298+4875C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.494

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11728802; hg19: chr4-14697492;