rs10516701

chr19-28001049-G-A

Variant summary

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

The NR_146733.1(LINC02987):n.360-3959G>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 0.0389 in 152,236 control chromosomes in the GnomAD database, including 201 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 0.039 (201 hom., cov: 31)
• Consequence: LINC02987 NR_146733.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

LINC02987 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02987	NR_146733.1	n.360-3959G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5918 AN: 152118 Hom.: 202 Cov.: 31

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0389 AC: 5918 AN: 152236 Hom.: 201 Cov.: 31 AF XY: 0.0413 AC XY: 3073 AN XY: 74450

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0425

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0150

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0411 Hom.: 83

Bravo AF: 0.0437

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.034
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516701; hg19: chr19-28491956;