chr4-188535079-T-G

Variant names:

• chr4-188535079-T-G
• rs7679676
• ENST00000503458.9:n.329+49214T>G

Variant summary

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

The ENST00000503458.9(LINC01060):​n.329+49214T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,054 control chromosomes in the GnomAD database, including 2,752 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 0.17 (2752 hom., cov: 32)
• Consequence: LINC01060 ENST00000503458.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 5 publications found

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

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 (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01060	NR_033869.1	n.342+49214T>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000503458.9	n.329+49214T>G		intron_variant	Intron 3 of 3	3
LINC01060	ENST00000503580.1	n.87+49214T>G		intron_variant	Intron 1 of 1	3
LINC01060	ENST00000510005.7	n.386+49214T>G		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26312 AN: 151936 Hom.: 2738 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.173 AC: 26350 AN: 152054 Hom.: 2752 Cov.: 32 AF XY: 0.173 AC XY: 12898 AN XY: 74340

African (AFR) AF: 0.283 AC: 11718 AN: 41426

American (AMR) AF: 0.111 AC: 1690 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.149 AC: 766 AN: 5154

South Asian (SAS) AF: 0.112 AC: 538 AN: 4816

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10586

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8785 AN: 67996

Other (OTH) AF: 0.143 AC: 302 AN: 2116

Alfa AF: 0.140 Hom.: 6991

Bravo AF: 0.170

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.096
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7679676; hg19: chr4-189456233;