rs7327426

Positions:

• chr13-61038606-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658247.1(LINC00378):​n.460+46250A>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00378	ENST00000658247.1	n.460+46250A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0629

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.266

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7327426; hg19: chr13-61612740;