1-200309631-A-G

Position:

• chr1-200309631-A-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00862	ENST00000636153.1	n.534-55560T>C		intron_variant, non_coding_transcript_variant		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;