1-83757355-A-G

Variant names:

• chr1-83757355-A-G
• rs6663404
• ENST00000417975.1:n.179-7056T>C

Variant summary

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

The ENST00000417975.1(LINC01725):​n.179-7056T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,058 control chromosomes in the GnomAD database, including 1,574 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 0.14 (1574 hom., cov: 32)
• Consequence: LINC01725 ENST00000417975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.949
• Publications: 0 publications found

Genes affected

LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01725	NR_119375.1	n.179-7056T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01725	ENST00000417975.1	n.179-7056T>C		intron_variant	Intron 1 of 2	1
LINC01725	ENST00000670031.2	n.207-7056T>C		intron_variant	Intron 1 of 2
LINC01725	ENST00000685925.2	n.236-7056T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20654 AN: 151940 Hom.: 1574 Cov.: 32

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.136 AC: 20655 AN: 152058 Hom.: 1574 Cov.: 32 AF XY: 0.134 AC XY: 9984 AN XY: 74314

African (AFR) AF: 0.0833 AC: 3456 AN: 41490

American (AMR) AF: 0.107 AC: 1637 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3468

East Asian (EAS) AF: 0.118 AC: 607 AN: 5162

South Asian (SAS) AF: 0.109 AC: 528 AN: 4824

European-Finnish (FIN) AF: 0.176 AC: 1862 AN: 10558

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11693 AN: 67966

Other (OTH) AF: 0.131 AC: 277 AN: 2110

Alfa AF: 0.154 Hom.: 1238

Bravo AF: 0.128

Asia WGS AF: 0.101 AC: 351 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.61
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs6663404; hg19: chr1-84223038;