rs7325568

Variant names:

• chr13-40244147-C-T
• rs7325568
• ENST00000615947.1:n.47-26397G>A

Variant summary

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

The ENST00000615947.1(LINC00598):​n.47-26397G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,808 control chromosomes in the GnomAD database, including 14,600 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 0.42 (14600 hom., cov: 31)
• Consequence: LINC00598 ENST00000615947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 publications found

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.581 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
LINC00598	ENST00000615947.1	n.47-26397G>A		intron_variant	Intron 1 of 3	4
LINC00598	ENST00000637438.1	n.401-37095G>A		intron_variant	Intron 2 of 3	5
LINC00598	ENST00000638084.1	n.406-26397G>A		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63457 AN: 151690 Hom.: 14602 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.418 AC: 63474 AN: 151808 Hom.: 14600 Cov.: 31 AF XY: 0.422 AC XY: 31317 AN XY: 74154

African (AFR) AF: 0.217 AC: 8972 AN: 41392

American (AMR) AF: 0.498 AC: 7597 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3466

East Asian (EAS) AF: 0.366 AC: 1888 AN: 5162

South Asian (SAS) AF: 0.599 AC: 2882 AN: 4810

European-Finnish (FIN) AF: 0.473 AC: 4961 AN: 10480

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34121 AN: 67930

Other (OTH) AF: 0.427 AC: 896 AN: 2100

Alfa AF: 0.459 Hom.: 19939

Bravo AF: 0.406

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.51
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7325568; hg19: chr13-40818284;