rs7327426

Variant names:

• chr13-61038606-A-T
• rs7327426
• ENST00000658247.1:n.460+46250A>T

Variant summary

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

The ENST00000658247.1(LINC00378):​n.460+46250A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,092 control chromosomes in the GnomAD database, including 5,487 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 0.26 (5487 hom., cov: 32)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 1 publications found

Genes affected

LINC00378 (HGNC:42704): (long intergenic non-protein coding RNA 378)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 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
LINC00378	ENST00000658247.1	n.460+46250A>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39054 AN: 151974 Hom.: 5487 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.257 AC: 39057 AN: 152092 Hom.: 5487 Cov.: 32 AF XY: 0.251 AC XY: 18652 AN XY: 74348

African (AFR) AF: 0.174 AC: 7232 AN: 41520

American (AMR) AF: 0.291 AC: 4437 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3468

East Asian (EAS) AF: 0.0629 AC: 324 AN: 5150

South Asian (SAS) AF: 0.201 AC: 972 AN: 4824

European-Finnish (FIN) AF: 0.230 AC: 2438 AN: 10592

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21706 AN: 67962

Other (OTH) AF: 0.266 AC: 561 AN: 2112

Alfa AF: 0.282 Hom.: 796

Bravo AF: 0.259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs7327426; hg19: chr13-61612740;