18-10622047-T-G

Variant names:

• chr18-10622047-T-G
• rs10502407
• ENST00000583691.2:n.198-5030A>C

Variant summary

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

The ENST00000584734.2(LINC01887):​n.1695+4182A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,086 control chromosomes in the GnomAD database, including 13,506 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 0.42 (13506 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01887 ENST00000584734.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489
• Publications: 2 publications found

Genes affected

LINC01887 (HGNC:52706): (long intergenic non-protein coding RNA 1887)

ENSG00000264503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584734.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01887	NR_146509.1		n.192+4182A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01887	ENST00000583691.2	TSL:5	n.198-5030A>C		intron	N/A
	LINC01887	ENST00000584734.2	TSL:3	n.1695+4182A>C		intron	N/A
	LINC01887	ENST00000743532.1		n.198-5030A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63528 AN: 151968 Hom.: 13492 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.418 AC: 63578 AN: 152086 Hom.: 13506 Cov.: 32 AF XY: 0.418 AC XY: 31086 AN XY: 74340

African (AFR) AF: 0.344 AC: 14251 AN: 41482

American (AMR) AF: 0.485 AC: 7423 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1572 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2411 AN: 5168

South Asian (SAS) AF: 0.573 AC: 2765 AN: 4824

European-Finnish (FIN) AF: 0.372 AC: 3926 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29767 AN: 67962

Other (OTH) AF: 0.462 AC: 976 AN: 2114

Alfa AF: 0.317 Hom.: 993

Bravo AF: 0.421

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	4.1
DANN	Benign	0.83
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10502407; hg19: chr18-10622044;