rs4146411

Positions:

• chr4-96344909-G-A
• chr4-96344909-G-C
• chr4-96344909-G-T

Variant summary

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

The ENST00000513393.1(LINC02267):​n.95-17951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,864 control chromosomes in the GnomAD database, including 2,767 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 0.15 (2767 hom., cov: 32)
• Consequence: LINC02267 ENST00000513393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

LINC02267 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02267	NR_147149.1	n.92+34115G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02267	ENST00000513393.1	n.95-17951G>A		intron_variant		3
LINC02267	ENST00000522173.1	n.63+34115G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22532 AN: 151746 Hom.: 2757 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0909

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.149 AC: 22554 AN: 151864 Hom.: 2767 Cov.: 32 AF XY: 0.154 AC XY: 11426 AN XY: 74192

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.0909

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.0662

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0900 Hom.: 2217

Bravo AF: 0.161

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.50
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4146411; hg19: chr4-97266060;