4-137206691-T-G

Position:

• chr4-137206691-T-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+6046A>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 0.155 in 151,866 control chromosomes in the GnomAD database, including 1,973 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 0.16 (1973 hom., cov: 32)
• Consequence: LINC02511 NR_149105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02511	NR_149105.1	n.63+6046A>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+6046A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23613 AN: 151748 Hom.: 1975 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.155 AC: 23611 AN: 151866 Hom.: 1973 Cov.: 32 AF XY: 0.157 AC XY: 11628 AN XY: 74234

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0888 Hom.: 153

Bravo AF: 0.154

Asia WGS AF: 0.161 AC: 558 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.56
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17644158; hg19: chr4-138127845;