4-10736406-T-C

Variant names:

• chr4-10736406-T-C
• rs7681266
• ENST00000720792.1:n.422+1548T>C

Variant summary

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

The ENST00000720792.1(LINC02498):​n.422+1548T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,996 control chromosomes in the GnomAD database, including 11,478 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 0.36 (11478 hom., cov: 32)
• Consequence: LINC02498 ENST00000720792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 2 publications found

Genes affected

LINC02498 (HGNC:53483): (long intergenic non-protein coding RNA 2498)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02498	ENST00000720792.1	n.422+1548T>C		intron_variant	Intron 2 of 2
LINC02498	ENST00000720793.1	n.323+1548T>C		intron_variant	Intron 2 of 2
LINC02498	ENST00000720794.1	n.399+1548T>C		intron_variant	Intron 2 of 2
LINC02498	ENST00000720795.1	n.298+1548T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54255 AN: 151876 Hom.: 11431 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.358 AC: 54346 AN: 151996 Hom.: 11478 Cov.: 32 AF XY: 0.356 AC XY: 26467 AN XY: 74306

African (AFR) AF: 0.597 AC: 24756 AN: 41456

American (AMR) AF: 0.250 AC: 3818 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1765 AN: 5160

South Asian (SAS) AF: 0.325 AC: 1563 AN: 4804

European-Finnish (FIN) AF: 0.305 AC: 3226 AN: 10560

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17352 AN: 67964

Other (OTH) AF: 0.358 AC: 754 AN: 2106

Alfa AF: 0.318 Hom.: 1092

Bravo AF: 0.361

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7681266; hg19: chr4-10738030;