chr1-58784780-A-G

Position:

• chr1-58784780-A-G

Variant summary

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

The ENST00000702469.1(ENSG00000290013):​n.156T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,880 control chromosomes in the GnomAD database, including 25,605 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 0.57 (25605 hom., cov: 31)
• Consequence: ENST00000702469.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

(HGNC:):

LINC01135 (HGNC:49450): (JUN divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702469.1	n.156T>C		non_coding_transcript_exon_variant	1/1
LINC01135	ENST00000685887.1	n.397A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85917 AN: 151758 Hom.: 25588 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.566 AC: 85965 AN: 151880 Hom.: 25605 Cov.: 31 AF XY: 0.573 AC XY: 42508 AN XY: 74216

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.555

Alfa AF: 0.568 Hom.: 2437

Bravo AF: 0.553

Asia WGS AF: 0.608 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646999; hg19: chr1-59250452;