rs1554615

Positions:

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

Variant summary

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

The ENST00000636153.1(LINC00862):​n.534-54882C>T 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 0.0328 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

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=-0.82).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00862	ENST00000636153.1	n.534-54882C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.00330

Gnomad4 AMR AF: 0.0437

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.00422

Gnomad4 OTH AF: 0.0326

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554615; hg19: chr1-200278081;