chr8-102535511-G-C

Variant names:

• chr8-102535511-G-C
• rs2033562
• ENST00000519630.1:n.228-222G>C

Variant summary

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

The ENST00000519630.1(LINC03047):​n.228-222G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,902 control chromosomes in the GnomAD database, including 24,364 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 0.56 (24364 hom., cov: 31)
• Consequence: LINC03047 ENST00000519630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 16 publications found

Genes affected

LINC03047 (HGNC:56265): (long intergenic non-protein coding RNA 3047)

LOC124901998 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901998	XR_007061039.1	n.189+713G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03047	ENST00000519630.1	n.228-222G>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85078 AN: 151784 Hom.: 24340 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.561 AC: 85151 AN: 151902 Hom.: 24364 Cov.: 31 AF XY: 0.557 AC XY: 41349 AN XY: 74250

African (AFR) AF: 0.449 AC: 18570 AN: 41396

American (AMR) AF: 0.565 AC: 8624 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1899 AN: 3468

East Asian (EAS) AF: 0.483 AC: 2496 AN: 5172

South Asian (SAS) AF: 0.486 AC: 2342 AN: 4822

European-Finnish (FIN) AF: 0.615 AC: 6475 AN: 10534

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42814 AN: 67934

Other (OTH) AF: 0.560 AC: 1180 AN: 2108

Alfa AF: 0.486 Hom.: 1412

Bravo AF: 0.556

Asia WGS AF: 0.532 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.61
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2033562; hg19: chr8-103547739;