rs10516701

Variant names:

• chr19-28001049-G-A
• rs10516701
• ENST00000748540.1:n.600-3959G>A

Variant summary

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

The ENST00000748540.1(LINC02987):​n.600-3959G>A variant causes a intron 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 ENST00000748540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 2 publications found

Genes affected

LINC02987 (HGNC:56093): (long intergenic non-protein coding RNA 2987)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02987	NR_146733.1	n.360-3959G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02987	ENST00000748540.1	n.600-3959G>A		intron_variant	Intron 6 of 7
LINC02987	ENST00000748541.1	n.1189-3959G>A		intron_variant	Intron 11 of 12
LINC02987	ENST00000748570.1	n.317-3959G>A		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.0478 AC: 1984 AN: 41536

American (AMR) AF: 0.0731 AC: 1119 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3470

East Asian (EAS) AF: 0.166 AC: 858 AN: 5162

South Asian (SAS) AF: 0.0425 AC: 205 AN: 4824

European-Finnish (FIN) AF: 0.0440 AC: 467 AN: 10612

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0150 AC: 1019 AN: 68010

Other (OTH) AF: 0.0378 AC: 80 AN: 2116

Alfa AF: 0.0397 Hom.: 93

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10516701; hg19: chr19-28491956;