rs7574012

chr2-37500087-G-Achr2-37500087-G-C

Variant summary

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

The ENST00000668683.1(ENSG00000287316):n.255-23882G>A 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 0.474 in 151,964 control chromosomes in the GnomAD database, including 17,273 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 0.47 (17273 hom., cov: 32)
• Consequence: ENST00000668683.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

(HGNC:):

LINC03063 (HGNC:56371): (long intergenic non-protein coding RNA 3063)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03063	XR_001739405.2	n.53-36908G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668683.1	n.255-23882G>A		intron_variant, non_coding_transcript_variant
LINC03063	ENST00000690322.2	n.129+10506G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71966 AN: 151846 Hom.: 17256 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.474 AC: 72023 AN: 151964 Hom.: 17273 Cov.: 32 AF XY: 0.472 AC XY: 35061 AN XY: 74268

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.471

Alfa AF: 0.458 Hom.: 2754

Bravo AF: 0.474

Asia WGS AF: 0.525 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7574012; hg19: chr2-37727230;