3-87143628-G-C

Variant names:

• chr3-87143628-G-C
• rs2088396
• ENST00000656042.1:n.3687G>C

Variant summary

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

The ENST00000656042.1(LINC00506):​n.3687G>C 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 0.38 in 152,006 control chromosomes in the GnomAD database, including 12,127 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 (12127 hom., cov: 33)
• Consequence: LINC00506 ENST00000656042.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 6 publications found

Genes affected

LINC00506 (HGNC:43557): (long intergenic non-protein coding RNA 506)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656042.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00506	NR_104153.1		n.329-10710G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00506	ENST00000656042.1		n.3687G>C		non_coding_transcript_exon	Exon 2 of 2
	LINC00506	ENST00000630120.3	TSL:4	n.648-10710G>C		intron	N/A
	LINC00506	ENST00000774842.1		n.575-13164G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57734 AN: 151888 Hom.: 12127 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.380 AC: 57740 AN: 152006 Hom.: 12127 Cov.: 33 AF XY: 0.377 AC XY: 27978 AN XY: 74296

African (AFR) AF: 0.201 AC: 8336 AN: 41476

American (AMR) AF: 0.382 AC: 5833 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1446 AN: 3462

East Asian (EAS) AF: 0.306 AC: 1585 AN: 5180

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4822

European-Finnish (FIN) AF: 0.459 AC: 4842 AN: 10544

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.482 AC: 32742 AN: 67932

Other (OTH) AF: 0.373 AC: 787 AN: 2110

Alfa AF: 0.296 Hom.: 823

Bravo AF: 0.368

Asia WGS AF: 0.309 AC: 1076 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.64
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2088396; hg19: chr3-87192778;