rs1324015

Positions:

• chr13-43153713-A-G
• chr13-43153713-A-T

Variant summary

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

The NR_047013.1(LINC00400):​n.120-4920A>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 0.631 in 151,782 control chromosomes in the GnomAD database, including 31,487 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 0.63 (31487 hom., cov: 29)
• Consequence: LINC00400 NR_047013.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

Genes affected

LINC00400 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00400	NR_047013.1	n.120-4920A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95691 AN: 151664 Hom.: 31420 Cov.: 29

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.631 AC: 95824 AN: 151782 Hom.: 31487 Cov.: 29 AF XY: 0.627 AC XY: 46508 AN XY: 74132

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.598

Alfa AF: 0.569 Hom.: 53854

Bravo AF: 0.656

Asia WGS AF: 0.647 AC: 2246 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.88
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324015; hg19: chr13-43727849;