chr3-127334018-C-A

Position:

• chr3-127334018-C-A

Variant summary

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

The ENST00000488425.1(LINC02016):​n.310-9287G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,004 control chromosomes in the GnomAD database, including 4,144 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 0.23 (4144 hom., cov: 32)
• Consequence: LINC02016 ENST00000488425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

LINC02016 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02016	NR_110147.1	n.310-9287G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02016	ENST00000488425.1	n.310-9287G>T		intron_variant		1
LINC02016	ENST00000654968.1	n.170-9287G>T		intron_variant
LINC02016	ENST00000663573.1	n.123+4201G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34508 AN: 151886 Hom.: 4141 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.227 AC: 34535 AN: 152004 Hom.: 4144 Cov.: 32 AF XY: 0.222 AC XY: 16457 AN XY: 74292

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.275

Alfa AF: 0.123 Hom.: 225

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2358551; hg19: chr3-127052861;