chr5-1374597-G-A

Position:

• chr5-1374597-G-A

Variant summary

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

The NR_125810.1(LINC01511):​n.512+4965C>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 0.745 in 152,102 control chromosomes in the GnomAD database, including 42,372 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 0.75 (42372 hom., cov: 32)
• Consequence: LINC01511 NR_125810.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

LINC01511 (HGNC:51200): (long intergenic non-protein coding RNA 1511)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01511	NR_125810.1	n.512+4965C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01511	ENST00000653645.1	n.436+4965C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113292 AN: 151984 Hom.: 42338 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.745 AC: 113374 AN: 152102 Hom.: 42372 Cov.: 32 AF XY: 0.749 AC XY: 55668 AN XY: 74362

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.737

Alfa AF: 0.721 Hom.: 12156

Bravo AF: 0.744

Asia WGS AF: 0.727 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs246995; hg19: chr5-1374712;