rs12771555

Positions:

• chr10-1173073-G-A
• chr10-1173073-G-C

Variant summary

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

The ENST00000655745.1(LINC00200):​n.264+12436G>A 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 0.288 in 152,032 control chromosomes in the GnomAD database, including 6,950 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 0.29 (6950 hom., cov: 32)
• Consequence: LINC00200 ENST00000655745.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800

Genes affected

LINC00200 (HGNC:30974): (long intergenic non-protein coding RNA 200)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 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
LINC00200	ENST00000655745.1	n.264+12436G>A		intron_variant, non_coding_transcript_variant
LINC00200	ENST00000652683.1	n.335-7604G>A		intron_variant, non_coding_transcript_variant
LINC00200	ENST00000666348.1	n.243+12436G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43721 AN: 151914 Hom.: 6946 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.288 AC: 43720 AN: 152032 Hom.: 6950 Cov.: 32 AF XY: 0.289 AC XY: 21483 AN XY: 74314

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.312

Alfa AF: 0.343 Hom.: 18915

Bravo AF: 0.267

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12771555; hg19: chr10-1219013; COSMIC: COSV60044430;