rs6728021

chr2-32896437-A-G

Variant summary

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

The ENST00000414054.5(LINC00486):n.290-2103A>G 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 0.0776 in 152,180 control chromosomes in the GnomAD database, including 544 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 0.078 (544 hom., cov: 32)
• Consequence: LINC00486 ENST00000414054.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569

Genes affected

LINC00486 (HGNC:42946): (long intergenic non-protein coding RNA 486)

LOC105374453 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374453	XR_939938.2	n.354+6300T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00486	ENST00000414054.5	n.290-2103A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11799 AN: 152062 Hom.: 544 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0150

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0776 AC: 11808 AN: 152180 Hom.: 544 Cov.: 32 AF XY: 0.0753 AC XY: 5603 AN XY: 74414

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0150

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.100 Hom.: 1669

Bravo AF: 0.0759

Asia WGS AF: 0.0130 AC: 46 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	11
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6728021; hg19: chr2-33121504;