chr1-112313948-C-T

Position:

• chr1-112313948-C-T

Variant summary

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

The ENST00000427290.2(LINC02884):​n.254+46414G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,124 control chromosomes in the GnomAD database, including 3,145 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 0.18 (3145 hom., cov: 32)
• Consequence: LINC02884 ENST00000427290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

LINC02884 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02884	NR_183465.1	n.246+46414G>A		intron_variant
LINC02884	NR_183466.1	n.246+46414G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02884	ENST00000427290.2	n.254+46414G>A		intron_variant		3
LINC02884	ENST00000654472.1	n.146-42343G>A		intron_variant
LINC02884	ENST00000658120.1	n.256+46414G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27511 AN: 152006 Hom.: 3146 Cov.: 32

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.181 AC: 27505 AN: 152124 Hom.: 3145 Cov.: 32 AF XY: 0.180 AC XY: 13366 AN XY: 74376

Gnomad4 AFR AF: 0.0499

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.189

Alfa AF: 0.243 Hom.: 7006

Bravo AF: 0.165

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7555668; hg19: chr1-112856570;