rs7662358

Variant names:

• chr4-188669705-C-A
• rs7662358
• ENST00000503580.1:n.88-11016C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-188669705-C-A
• chr4-188669705-C-G
• chr4-188669705-C-T

Variant summary

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

The ENST00000503580.1(LINC01060):​n.88-11016C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,484 control chromosomes in the GnomAD database, including 2,069 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 0.16 (2069 hom., cov: 32)
• Consequence: LINC01060 ENST00000503580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503580.1. 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
	LINC01060	ENST00000503580.1	TSL:3	n.88-11016C>A		intron	N/A
	LINC01060	ENST00000664177.2		n.338-10578C>A		intron	N/A
	LINC01060	ENST00000692519.2		n.389-10578C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24569 AN: 151366 Hom.: 2064 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.162 AC: 24599 AN: 151484 Hom.: 2069 Cov.: 32 AF XY: 0.158 AC XY: 11664 AN XY: 74000

African (AFR) AF: 0.186 AC: 7669 AN: 41252

American (AMR) AF: 0.145 AC: 2207 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3466

East Asian (EAS) AF: 0.107 AC: 547 AN: 5128

South Asian (SAS) AF: 0.117 AC: 559 AN: 4796

European-Finnish (FIN) AF: 0.139 AC: 1457 AN: 10458

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11371 AN: 67858

Other (OTH) AF: 0.169 AC: 356 AN: 2108

Alfa AF: 0.158 Hom.: 3037

Bravo AF: 0.161

Asia WGS AF: 0.119 AC: 412 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	3.3
DANN	Benign	0.76
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7662358; hg19: chr4-189590859;