rs7679676

Positions:

• chr4-188535079-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033869.1(LINC01060):​n.342+49214T>G variant causes a intron, non coding transcript 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 NR_033869.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01060	NR_033869.1	n.342+49214T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01060	ENST00000664177.1	n.330+49214T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.143

Alfa AF: 0.134 Hom.: 3054

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7679676; hg19: chr4-189456233;