4-138288547-G-T

Variant names:

• chr4-138288547-G-T
• rs6817763
• ENST00000751419.1:n.236-1735C>A

Variant summary

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

The ENST00000751419.1(LINC00498):​n.236-1735C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,786 control chromosomes in the GnomAD database, including 21,698 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 0.53 (21698 hom., cov: 31)
• Consequence: LINC00498 ENST00000751419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 7 publications found

Genes affected

LINC00498 (HGNC:43435): (long intergenic non-protein coding RNA 498)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751419.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00498	NR_198994.1		n.600-1735C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00498	ENST00000751419.1		n.236-1735C>A		intron	N/A
	LINC00498	ENST00000751420.1		n.236-1739C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80960 AN: 151668 Hom.: 21684 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.534 AC: 81026 AN: 151786 Hom.: 21698 Cov.: 31 AF XY: 0.537 AC XY: 39834 AN XY: 74162

African (AFR) AF: 0.589 AC: 24387 AN: 41394

American (AMR) AF: 0.565 AC: 8592 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1637 AN: 3464

East Asian (EAS) AF: 0.523 AC: 2686 AN: 5134

South Asian (SAS) AF: 0.446 AC: 2142 AN: 4808

European-Finnish (FIN) AF: 0.591 AC: 6235 AN: 10550

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.496 AC: 33688 AN: 67916

Other (OTH) AF: 0.516 AC: 1088 AN: 2108

Alfa AF: 0.503 Hom.: 72964

Bravo AF: 0.535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.62
DANN	Benign	0.47
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6817763; hg19: chr4-139209701;