chr13-74421523-A-G

Position:

• chr13-74421523-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_047005.1(LINC00381):​n.153+1984A>G 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 0.0564 in 152,322 control chromosomes in the GnomAD database, including 353 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 0.056 (353 hom., cov: 32)
• Consequence: LINC00381 NR_047005.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.72

Genes affected

LINC00381 (HGNC:42708): (long intergenic non-protein coding RNA 381)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00381	NR_047005.1	n.153+1984A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00381	ENST00000649990.1	n.71+2295A>G		intron_variant, non_coding_transcript_variant
LINC00381	ENST00000423629.1	n.153+1984A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8594 AN: 152204 Hom.: 353 Cov.: 32

Gnomad AFR AF: 0.0148

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0527

Gnomad FIN AF: 0.0897

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0564 AC: 8594 AN: 152322 Hom.: 353 Cov.: 32 AF XY: 0.0562 AC XY: 4183 AN XY: 74484

Gnomad4 AFR AF: 0.0147

Gnomad4 AMR AF: 0.0473

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0530

Gnomad4 FIN AF: 0.0897

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0753 Hom.: 526

Bravo AF: 0.0507

Asia WGS AF: 0.0240 AC: 84 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17714988; hg19: chr13-74995660;