rs17043944

Variant names:

• chr2-22501721-C-T
• rs17043944
• ENST00000450551.1:n.70+29315G>A

Variant summary

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

The ENST00000450551.1(LINC01830):​n.70+29315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0387 in 152,118 control chromosomes in the GnomAD database, including 234 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 0.039 (234 hom., cov: 32)
• Consequence: LINC01830 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 1 publications found

Genes affected

LINC01830 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0997 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
LINC01830	ENST00000450551.1	n.70+29315G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5883 AN: 152000 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.000584

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0387 AC: 5893 AN: 152118 Hom.: 234 Cov.: 32 AF XY: 0.0389 AC XY: 2892 AN XY: 74370

African (AFR) AF: 0.0869 AC: 3605 AN: 41508

American (AMR) AF: 0.0209 AC: 319 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00922 AC: 32 AN: 3472

East Asian (EAS) AF: 0.000585 AC: 3 AN: 5126

South Asian (SAS) AF: 0.107 AC: 517 AN: 4818

European-Finnish (FIN) AF: 0.00725 AC: 77 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0185 AC: 1260 AN: 67984

Other (OTH) AF: 0.0303 AC: 64 AN: 2114

Alfa AF: 0.0204 Hom.: 94

Bravo AF: 0.0395

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.71
PhyloP100		0.50
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17043944; hg19: chr2-22724593;