1-63015059-C-G

Variant names:

• chr1-63015059-C-G
• rs17124318
• ENST00000641712.1:n.745+1603G>C

Variant summary

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

The ENST00000641712.1(LINC01739):​n.745+1603G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 152,218 control chromosomes in the GnomAD database, including 254 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 0.040 (254 hom., cov: 32)
• Consequence: LINC01739 ENST00000641712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 9 publications found

Genes affected

LINC01739 (HGNC:52527): (long intergenic non-protein coding RNA 1739)

ENSG00000286455 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01739	ENST00000641712.1	n.745+1603G>C		intron_variant	Intron 3 of 3
ENSG00000286455	ENST00000663274.1	n.211-961C>G		intron_variant	Intron 2 of 4
LINC01739	ENST00000748522.1	n.254-38848G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6044 AN: 152102 Hom.: 252 Cov.: 32

Gnomad AFR AF: 0.00995

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0196

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0398 AC: 6052 AN: 152218 Hom.: 254 Cov.: 32 AF XY: 0.0426 AC XY: 3174 AN XY: 74426

African (AFR) AF: 0.00992 AC: 412 AN: 41544

American (AMR) AF: 0.0378 AC: 578 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3470

East Asian (EAS) AF: 0.143 AC: 743 AN: 5184

South Asian (SAS) AF: 0.215 AC: 1033 AN: 4810

European-Finnish (FIN) AF: 0.0196 AC: 208 AN: 10612

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2756 AN: 68006

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0396 Hom.: 83

Bravo AF: 0.0371

Asia WGS AF: 0.175 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.40
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs17124318; hg19: chr1-63480730;