18-22074176-A-G

Variant names:

• chr18-22074176-A-G
• rs4800353
• ENST00000716236.1:n.348-4671A>G

Variant summary

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

The ENST00000716236.1(LINC01900):​n.348-4671A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,120 control chromosomes in the GnomAD database, including 9,680 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 (9680 hom., cov: 32)
• Consequence: LINC01900 ENST00000716236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 8 publications found

Genes affected

LINC01900 (HGNC:52719): (long intergenic non-protein coding RNA 1900)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716236.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01900	ENST00000716236.1		n.348-4671A>G		intron	N/A
	LINC01900	ENST00000780669.1		n.349-24195A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44265 AN: 152002 Hom.: 9643 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.292 AC: 44352 AN: 152120 Hom.: 9680 Cov.: 32 AF XY: 0.291 AC XY: 21625 AN XY: 74362

African (AFR) AF: 0.597 AC: 24779 AN: 41480

American (AMR) AF: 0.346 AC: 5282 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1329 AN: 5176

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1571 AN: 10596

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9148 AN: 67992

Other (OTH) AF: 0.269 AC: 568 AN: 2108

Alfa AF: 0.191 Hom.: 13306

Bravo AF: 0.320

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4800353; hg19: chr18-19654137;