chr4-149163733-G-A

Position:

• chr4-149163733-G-A

Variant summary

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

The NR_125887.1(LINC02355):​n.599+8008G>A 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 0.0729 in 152,080 control chromosomes in the GnomAD database, including 1,212 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 0.073 (1212 hom., cov: 32)
• Consequence: LINC02355 NR_125887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

Genes affected

LINC02355 (HGNC:53277): (long intergenic non-protein coding RNA 2355)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02355	NR_125887.1	n.599+8008G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02355	ENST00000503100.1	n.599+8008G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11043 AN: 151962 Hom.: 1199 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.00227

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.00501

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0729 AC: 11090 AN: 152080 Hom.: 1212 Cov.: 32 AF XY: 0.0694 AC XY: 5161 AN XY: 74334

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0296

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.00975

Gnomad4 FIN AF: 0.00227

Gnomad4 NFE AF: 0.00501

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0462 Hom.: 103

Bravo AF: 0.0819

Asia WGS AF: 0.0540 AC: 189 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6842217; hg19: chr4-150084885;