ENST00000844361.1:n.200-3656C>G

Variant names:

• chr17-60559102-C-G
• rs1197065
• ENST00000844361.1:n.200-3656C>G

Variant summary

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

The ENST00000844361.1(LINC01999):​n.200-3656C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,254 control chromosomes in the GnomAD database, including 11,450 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 0.24 (11450 hom., cov: 32)
• Consequence: LINC01999 ENST00000844361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 3 publications found

Genes affected

LINC01999 (HGNC:52834): (long intergenic non-protein coding RNA 1999)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 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
LINC01999	ENST00000844361.1	n.200-3656C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35987 AN: 152136 Hom.: 11410 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.237 AC: 36078 AN: 152254 Hom.: 11450 Cov.: 32 AF XY: 0.228 AC XY: 17003 AN XY: 74444

African (AFR) AF: 0.729 AC: 30279 AN: 41520

American (AMR) AF: 0.116 AC: 1768 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 252 AN: 3468

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5180

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4828

European-Finnish (FIN) AF: 0.0247 AC: 262 AN: 10614

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0413 AC: 2807 AN: 68026

Other (OTH) AF: 0.185 AC: 392 AN: 2114

Alfa AF: 0.0209 Hom.: 22

Bravo AF: 0.268

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.21
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1197065; hg19: chr17-58636463;