4-14697498-T-C

Position:

• chr4-14697498-T-C

Variant summary

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

The ENST00000509654.5(LINC00504):​n.184-125252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,160 control chromosomes in the GnomAD database, including 45,683 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 0.77 (45683 hom., cov: 32)
• Consequence: LINC00504 ENST00000509654.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

Genes affected

LINC00504 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00504	NR_126435.1	n.224+3245A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00504	ENST00000509654.5	n.184-125252A>G		intron_variant		1
LINC00504	ENST00000505089.6	n.224+3245A>G		intron_variant		2
LINC00504	ENST00000506292.2	n.237+3245A>G		intron_variant		2
LINC00504	ENST00000515031.5	n.298+3245A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117016 AN: 152042 Hom.: 45648 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.770 AC: 117109 AN: 152160 Hom.: 45683 Cov.: 32 AF XY: 0.772 AC XY: 57447 AN XY: 74384

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.779

Alfa AF: 0.807 Hom.: 21645

Bravo AF: 0.771

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4698280; hg19: chr4-14699122;