19-30849845-A-G

Variant names:

• chr19-30849845-A-G
• rs17545624
• ENST00000716200.1:n.216-56569A>G

Variant summary

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

The ENST00000716200.1(LINC01834):​n.216-56569A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,054 control chromosomes in the GnomAD database, including 3,573 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 0.19 (3573 hom., cov: 32)
• Consequence: LINC01834 ENST00000716200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24
• Publications: 4 publications found

Genes affected

LINC01834 (HGNC:52648): (long intergenic non-protein coding RNA 1834)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716200.1. 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
	LINC01834	ENST00000716200.1		n.216-56569A>G		intron	N/A
	LINC01834	ENST00000716201.1		n.165-22202A>G		intron	N/A
	LINC01834	ENST00000824349.1		n.131-22202A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29290 AN: 151936 Hom.: 3574 Cov.: 32

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.193 AC: 29285 AN: 152054 Hom.: 3573 Cov.: 32 AF XY: 0.185 AC XY: 13740 AN XY: 74304

African (AFR) AF: 0.0819 AC: 3400 AN: 41490

American (AMR) AF: 0.146 AC: 2229 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3470

East Asian (EAS) AF: 0.0204 AC: 106 AN: 5186

South Asian (SAS) AF: 0.0915 AC: 440 AN: 4810

European-Finnish (FIN) AF: 0.209 AC: 2200 AN: 10528

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19362 AN: 67992

Other (OTH) AF: 0.176 AC: 370 AN: 2106

Alfa AF: 0.244 Hom.: 7873

Bravo AF: 0.182

Asia WGS AF: 0.0680 AC: 237 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.6
DANN	Benign	0.57
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs17545624; hg19: chr19-31340752;