18-75702957-G-T

Variant names:

• chr18-75702957-G-T
• rs7233038
• ENST00000564156.1:n.371-5346C>A

Variant summary

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

The ENST00000564156.1(LINC01898):​n.371-5346C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,086 control chromosomes in the GnomAD database, including 2,953 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 (2953 hom., cov: 32)
• Consequence: LINC01898 ENST00000564156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 1 publications found

Genes affected

LINC01898 (HGNC:52717): (long intergenic non-protein coding RNA 1898)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01898	NR_134646.1	n.389-5346C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01898	ENST00000564156.1	n.371-5346C>A		intron_variant	Intron 1 of 1	1
LINC01898	ENST00000662237.1	n.393-5346C>A		intron_variant	Intron 1 of 2
LINC01898	ENST00000662762.1	n.837-5346C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29586 AN: 151968 Hom.: 2956 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.195 AC: 29585 AN: 152086 Hom.: 2953 Cov.: 32 AF XY: 0.194 AC XY: 14423 AN XY: 74354

African (AFR) AF: 0.178 AC: 7369 AN: 41484

American (AMR) AF: 0.205 AC: 3131 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1684 AN: 5156

South Asian (SAS) AF: 0.128 AC: 614 AN: 4810

European-Finnish (FIN) AF: 0.192 AC: 2032 AN: 10588

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13387 AN: 67970

Other (OTH) AF: 0.210 AC: 443 AN: 2112

Alfa AF: 0.190 Hom.: 8938

Bravo AF: 0.196

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.74
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs7233038; hg19: chr18-73414912;