4-14875438-A-T

Variant names:

• chr4-14875438-A-T
• rs923985
• ENST00000509654.5:n.109+12621T>A

Variant summary

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

The ENST00000509654.5(LINC00504):​n.109+12621T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,984 control chromosomes in the GnomAD database, including 14,469 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 0.44 (14469 hom., cov: 32)
• Consequence: LINC00504 ENST00000509654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00504	NR_126435.1	n.111+12621T>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00504	ENST00000509654.5	n.109+12621T>A		intron_variant	Intron 1 of 4	1
LINC00504	ENST00000505089.6	n.111+12621T>A		intron_variant	Intron 1 of 6	2
LINC00504	ENST00000515031.5	n.110+12621T>A		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66095 AN: 151868 Hom.: 14450 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.435 AC: 66153 AN: 151984 Hom.: 14469 Cov.: 32 AF XY: 0.430 AC XY: 31972 AN XY: 74292

African (AFR) AF: 0.492 AC: 20402 AN: 41450

American (AMR) AF: 0.414 AC: 6329 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1639 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1480 AN: 5164

South Asian (SAS) AF: 0.422 AC: 2025 AN: 4804

European-Finnish (FIN) AF: 0.370 AC: 3909 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29025 AN: 67932

Other (OTH) AF: 0.429 AC: 905 AN: 2110

Alfa AF: 0.425 Hom.: 1669

Bravo AF: 0.442

Asia WGS AF: 0.386 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs923985; hg19: chr4-14877062;