rs350993

Positions:

• chr4-131574942-A-G
• chr4-131574942-A-T

Variant summary

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

The NR_183917.1(LINC02377):​n.645-46933A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,752 control chromosomes in the GnomAD database, including 28,143 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 0.59 (28143 hom., cov: 31)
• Consequence: LINC02377 NR_183917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

LINC02377 (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 (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02377	NR_183917.1	n.645-46933A>G		intron_variant
LINC02377	NR_183918.1	n.852-46933A>G		intron_variant
LINC02377	NR_183919.1	n.763-46933A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02377	ENST00000654488.1	n.849-16328A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90271 AN: 151634 Hom.: 28151 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.595 AC: 90281 AN: 151752 Hom.: 28143 Cov.: 31 AF XY: 0.597 AC XY: 44260 AN XY: 74172

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.593

Alfa AF: 0.664 Hom.: 34382

Bravo AF: 0.583

Asia WGS AF: 0.547 AC: 1903 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	0.33
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs350993; hg19: chr4-132496097;