3-87143628-G-C

Position:

• chr3-87143628-G-C

Variant summary

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

The NR_104153.1(LINC00506):​n.329-10710G>C 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 0.38 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 NR_104153.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

LINC00506 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00506	NR_104153.1	n.329-10710G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00506	ENST00000630120.2	n.403-10710G>C		intron_variant, non_coding_transcript_variant		4
LINC00506	ENST00000656042.1	n.3687G>C		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.373

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2088396; hg19: chr3-87192778;