4-6670232-T-C

Variant names:

• chr4-6670232-T-C
• rs724858
• ENST00000654965.1:n.1028A>G

Variant summary

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

The ENST00000654965.1(LINC02482):​n.1028A>G variant causes a non coding transcript exon 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 ENST00000654965.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 13 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02482	ENST00000654965.1	n.1028A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02482	ENST00000656634.1	n.1050A>G		non_coding_transcript_exon_variant	Exon 2 of 2
MRFAP1L2	ENST00000645429.1	n.295-4761T>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.206 AC: 8557 AN: 41482

American (AMR) AF: 0.432 AC: 6607 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1348 AN: 3466

East Asian (EAS) AF: 0.143 AC: 740 AN: 5178

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4814

European-Finnish (FIN) AF: 0.559 AC: 5891 AN: 10542

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30695 AN: 67940

Other (OTH) AF: 0.377 AC: 794 AN: 2108

Alfa AF: 0.422 Hom.: 22929

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs724858; hg19: chr4-6671959;