5-80621698-A-G

Position:

• chr5-80621698-A-G

Variant summary

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

The NR_125754.1(LINC01337):​n.117+710T>C 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 0.242 in 151,994 control chromosomes in the GnomAD database, including 4,641 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 0.24 (4641 hom., cov: 31)
• Consequence: LINC01337 NR_125754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

Genes affected

LINC01337 (HGNC:50546): (long intergenic non-protein coding RNA 1337)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01337	NR_125754.1	n.117+710T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01337	ENST00000515871.1	n.117+710T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36817 AN: 151876 Hom.: 4635 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.242 AC: 36843 AN: 151994 Hom.: 4641 Cov.: 31 AF XY: 0.239 AC XY: 17767 AN XY: 74316

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.261

Alfa AF: 0.264 Hom.: 5478

Bravo AF: 0.243

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.6
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1222809; hg19: chr5-79917517;