rs1554615

Variant names:

• chr1-200308953-G-A
• rs1554615
• ENST00000636153.1:n.534-54882C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-200308953-G-A
• chr1-200308953-G-C

Variant summary

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

The ENST00000636153.1(LINC00862):​n.534-54882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 152,256 control chromosomes in the GnomAD database, including 677 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 0.033 (677 hom., cov: 32)
• Consequence: LINC00862 ENST00000636153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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.534-54882C>T		intron_variant	Intron 4 of 4	5
LINC00862	ENST00000760608.1	n.195-63489C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 4989 AN: 152138 Hom.: 679 Cov.: 32

Gnomad AFR AF: 0.00326

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00422

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0328 AC: 4991 AN: 152256 Hom.: 677 Cov.: 32 AF XY: 0.0412 AC XY: 3065 AN XY: 74436

African (AFR) AF: 0.00330 AC: 137 AN: 41566

American (AMR) AF: 0.0437 AC: 669 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 33 AN: 3468

East Asian (EAS) AF: 0.445 AC: 2297 AN: 5164

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4822

European-Finnish (FIN) AF: 0.0452 AC: 480 AN: 10608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00422 AC: 287 AN: 68012

Other (OTH) AF: 0.0326 AC: 69 AN: 2114

Alfa AF: 0.0162 Hom.: 22

Bravo AF: 0.0305

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.50
DANN	Benign	0.72
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1554615; hg19: chr1-200278081;