rs1015140

Variant names:

• chr1-200309631-A-G
• rs1015140
• ENST00000636153.1:n.534-55560T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-200309631-A-G
• chr1-200309631-A-T

Variant summary

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

The ENST00000636153.1(LINC00862):​n.534-55560T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0338 in 152,288 control chromosomes in the GnomAD database, including 621 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 0.034 (621 hom., cov: 32)
• Consequence: LINC00862 ENST00000636153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

LINC00862 (HGNC:21901): (long intergenic non-protein coding RNA 862) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00862	ENST00000636153.1	n.534-55560T>C		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5143 AN: 152170 Hom.: 622 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00398

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0338 AC: 5147 AN: 152288 Hom.: 621 Cov.: 32 AF XY: 0.0418 AC XY: 3113 AN XY: 74468

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.0439

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.00398

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0101 Hom.: 87

Bravo AF: 0.0322

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015140; hg19: chr1-200278759;