chr5-38056651-A-C

Position:

• chr5-38056651-A-C

Variant summary

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

The NR_147009.1(LINC02107):​n.233+27595A>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 0.198 in 152,102 control chromosomes in the GnomAD database, including 3,151 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 0.20 (3151 hom., cov: 32)
• Consequence: LINC02107 NR_147009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

LINC02119 (HGNC:52975): (long intergenic non-protein coding RNA 2119)

LINC02107 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02107	NR_147009.1	n.233+27595A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02119	ENST00000669275.1	n.313+27595A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30086 AN: 151984 Hom.: 3140 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.198 AC: 30125 AN: 152102 Hom.: 3151 Cov.: 32 AF XY: 0.202 AC XY: 14982 AN XY: 74340

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.162

Alfa AF: 0.179 Hom.: 4810

Bravo AF: 0.190

Asia WGS AF: 0.140 AC: 488 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	2.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512674; hg19: chr5-38056753;