10-1173073-G-A

Variant names:

• chr10-1173073-G-A
• rs12771555
• ENST00000652683.1:n.335-7604G>A

Variant summary

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

The ENST00000652683.1(LINC00200):​n.335-7604G>A variant causes a intron 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 ENST00000652683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652683.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00200	ENST00000652683.1		n.335-7604G>A		intron	N/A
	LINC00200	ENST00000655745.1		n.264+12436G>A		intron	N/A
	LINC00200	ENST00000666348.1		n.243+12436G>A		intron	N/A

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

African (AFR) AF: 0.153 AC: 6343 AN: 41470

American (AMR) AF: 0.227 AC: 3467 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1745 AN: 5160

South Asian (SAS) AF: 0.474 AC: 2280 AN: 4814

European-Finnish (FIN) AF: 0.318 AC: 3365 AN: 10580

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24151 AN: 67942

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.335 Hom.: 38411

Bravo AF: 0.267

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.69
PhyloP100		0.80

Splicing

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

Other links and lift over

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