rs9317297

Positions:

• chr13-63247365-G-A

Variant summary

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

The NR_126409.1(LINC00376):​n.215-15234C>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 0.0811 in 152,054 control chromosomes in the GnomAD database, including 681 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 0.081 (681 hom., cov: 32)
• Consequence: LINC00376 NR_126409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

LINC00376 (HGNC:42701): (long intergenic non-protein coding RNA 376)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00376	NR_126409.1	n.215-15234C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00376	ENST00000439454.3	n.250-15234C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0812 AC: 12331 AN: 151934 Hom.: 679 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.0811 AC: 12336 AN: 152054 Hom.: 681 Cov.: 32 AF XY: 0.0839 AC XY: 6235 AN XY: 74310

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0910

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0920

Gnomad4 OTH AF: 0.0786

Alfa AF: 0.0923 Hom.: 368

Bravo AF: 0.0848

Asia WGS AF: 0.0850 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317297; hg19: chr13-63821498;