1-63060085-C-T

Variant names:

• chr1-63060085-C-T
• rs1888176
• ENST00000748522.1:n.253+14345G>A

Variant summary

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

The ENST00000748522.1(LINC01739):​n.253+14345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,046 control chromosomes in the GnomAD database, including 14,910 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 0.44 (14910 hom., cov: 33)
• Consequence: LINC01739 ENST00000748522.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 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	ENST00000748522.1	n.253+14345G>A		intron_variant	Intron 1 of 1
LINC01739	ENST00000748523.1	n.192+14345G>A		intron_variant	Intron 1 of 4
LINC01739	ENST00000748524.1	n.104+14345G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66247 AN: 151928 Hom.: 14877 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.436 AC: 66318 AN: 152046 Hom.: 14910 Cov.: 33 AF XY: 0.436 AC XY: 32377 AN XY: 74300

African (AFR) AF: 0.531 AC: 22021 AN: 41444

American (AMR) AF: 0.490 AC: 7487 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3472

East Asian (EAS) AF: 0.278 AC: 1437 AN: 5176

South Asian (SAS) AF: 0.414 AC: 1999 AN: 4826

European-Finnish (FIN) AF: 0.387 AC: 4088 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26763 AN: 67958

Other (OTH) AF: 0.416 AC: 879 AN: 2114

Alfa AF: 0.405 Hom.: 19493

Bravo AF: 0.451

Asia WGS AF: 0.397 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.2
DANN	Benign	0.80
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1888176; hg19: chr1-63525756; COSMIC: COSV59948050;