rs8098673

Variant names:

• chr18-22093370-A-C
• rs8098673
• ENST00000579830.1:n.44-5001A>C

Your query was ambiguous. Multiple possible variants found:

• chr18-22093370-A-C
• chr18-22093370-A-T

Variant summary

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

The ENST00000579830.1(LINC01900):​n.44-5001A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,086 control chromosomes in the GnomAD database, including 14,170 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 0.42 (14170 hom., cov: 33)
• Consequence: LINC01900 ENST00000579830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 9 publications found

Genes affected

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

GATA6-AS1 (HGNC:48840): (GATA6 antisense RNA 1 (head to head))

LOC124904259 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579830.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01900	ENST00000579830.1	TSL:3	n.44-5001A>C		intron	N/A
	LINC01900	ENST00000716236.1		n.442-5001A>C		intron	N/A
	LINC01900	ENST00000716240.1		n.345+1485A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64026 AN: 151968 Hom.: 14140 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.421 AC: 64101 AN: 152086 Hom.: 14170 Cov.: 33 AF XY: 0.428 AC XY: 31841 AN XY: 74334

African (AFR) AF: 0.513 AC: 21280 AN: 41486

American (AMR) AF: 0.546 AC: 8350 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1181 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2142 AN: 5176

South Asian (SAS) AF: 0.433 AC: 2086 AN: 4816

European-Finnish (FIN) AF: 0.435 AC: 4596 AN: 10562

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22999 AN: 67978

Other (OTH) AF: 0.439 AC: 927 AN: 2114

Alfa AF: 0.355 Hom.: 7278

Bravo AF: 0.436

Asia WGS AF: 0.486 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.44
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs8098673; hg19: chr18-19673331;