rs7552393

Variant names:

• chr1-83788868-A-G
• rs7552393
• ENST00000417975.1:n.179-38569T>C

Variant summary

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

The ENST00000417975.1(LINC01725):​n.179-38569T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,944 control chromosomes in the GnomAD database, including 24,627 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 0.56 (24627 hom., cov: 32)
• Consequence: LINC01725 ENST00000417975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 11 publications found

Genes affected

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

ENSG00000237076 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01725	NR_119375.1	n.179-38569T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01725	ENST00000417975.1	n.179-38569T>C		intron_variant	Intron 1 of 2	1
LINC01725	ENST00000670031.2	n.207-38569T>C		intron_variant	Intron 1 of 2
LINC01725	ENST00000685925.2	n.236-38569T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84913 AN: 151824 Hom.: 24587 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.559 AC: 84996 AN: 151944 Hom.: 24627 Cov.: 32 AF XY: 0.550 AC XY: 40859 AN XY: 74284

African (AFR) AF: 0.675 AC: 27965 AN: 41434

American (AMR) AF: 0.384 AC: 5869 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1653 AN: 5156

South Asian (SAS) AF: 0.450 AC: 2169 AN: 4822

European-Finnish (FIN) AF: 0.540 AC: 5711 AN: 10584

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38325 AN: 67888

Other (OTH) AF: 0.505 AC: 1066 AN: 2112

Alfa AF: 0.554 Hom.: 79215

Bravo AF: 0.548

Asia WGS AF: 0.381 AC: 1325 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7552393; hg19: chr1-84254551; COSMIC: COSV107519965;