4-6670232-T-C

Position:

• chr4-6670232-T-C

Variant summary

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

The ENST00000647523.2(LINC02482):​n.213+3452A>G 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 0.375 in 152,016 control chromosomes in the GnomAD database, including 11,950 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 0.38 (11950 hom., cov: 33)
• Consequence: LINC02482 ENST00000647523.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

LINC02482 (HGNC:53458): (long intergenic non-protein coding RNA 2482)

MRFAP1L2 (HGNC:25109): (Morf4 family associated protein 1 like 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02482	ENST00000647523.2	n.213+3452A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57034 AN: 151898 Hom.: 11946 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.375 AC: 57044 AN: 152016 Hom.: 11950 Cov.: 33 AF XY: 0.380 AC XY: 28209 AN XY: 74296

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.377

Alfa AF: 0.427 Hom.: 18440

Bravo AF: 0.358

Asia WGS AF: 0.280 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
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: rs724858; hg19: chr4-6671959;