chr4-177765942-C-G

Variant names:

• chr4-177765942-C-G
• rs1902018
• ENST00000507870.1:n.374+33463C>G

Variant summary

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

The ENST00000507870.1(LINC01098):​n.374+33463C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,112 control chromosomes in the GnomAD database, including 4,454 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 0.22 (4454 hom., cov: 32)
• Consequence: LINC01098 ENST00000507870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 1 publications found

Genes affected

LINC01098 (HGNC:27731): (long intergenic non-protein coding RNA 1098)

LINC01099 (HGNC:49222): (long intergenic non-protein coding RNA 1099)

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 (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01098	NR_028342.1	n.374+33463C>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01098	ENST00000507870.1	n.374+33463C>G		intron_variant	Intron 2 of 5	1
LINC01099	ENST00000507011.1	n.143-7556G>C		intron_variant	Intron 2 of 4	5
LINC01098	ENST00000666825.1	n.374+33463C>G		intron_variant	Intron 2 of 2
LINC01099	ENST00000798945.1	n.250+763G>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33705 AN: 151992 Hom.: 4446 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.222 AC: 33722 AN: 152112 Hom.: 4454 Cov.: 32 AF XY: 0.224 AC XY: 16641 AN XY: 74332

African (AFR) AF: 0.0795 AC: 3304 AN: 41538

American (AMR) AF: 0.344 AC: 5259 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1174 AN: 5154

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4814

European-Finnish (FIN) AF: 0.272 AC: 2874 AN: 10580

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17995 AN: 67960

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.142 Hom.: 308

Bravo AF: 0.220

Asia WGS AF: 0.328 AC: 1142 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	2.6
DANN	Benign	0.53
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1902018; hg19: chr4-178687096;