rs75900745

Positions:

• chr4-137169858-A-G

Variant summary

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

The NR_149105.1(LINC02511):​n.63+42879T>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 0.0794 in 152,188 control chromosomes in the GnomAD database, including 566 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 0.079 (566 hom., cov: 31)
• Consequence: LINC02511 NR_149105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

Genes affected

LINC02511 (HGNC:53500): (long intergenic non-protein coding RNA 2511)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02511	NR_149105.1	n.63+42879T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02511	ENST00000656956.1	n.37+42879T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0794 AC: 12082 AN: 152072 Hom.: 566 Cov.: 31

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0779

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0794 AC: 12083 AN: 152188 Hom.: 566 Cov.: 31 AF XY: 0.0830 AC XY: 6177 AN XY: 74414

Gnomad4 AFR AF: 0.0505

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.0811

Alfa AF: 0.0830 Hom.: 72

Bravo AF: 0.0769

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75900745; hg19: chr4-138091012;