rs1964033

Positions:

• chr4-131665703-C-A

Variant summary

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

The NR_183920.1(LINC02377):​n.785-27631C>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 0.492 in 151,942 control chromosomes in the GnomAD database, including 18,673 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 0.49 (18673 hom., cov: 32)
• Consequence: LINC02377 NR_183920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

Genes affected

LINC02377 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02377	NR_183920.1	n.785-27631C>A		intron_variant, non_coding_transcript_variant
LINC02377	NR_183917.1	n.772-27631C>A		intron_variant, non_coding_transcript_variant
LINC02377	NR_183918.1	n.979-27631C>A		intron_variant, non_coding_transcript_variant
LINC02377	NR_183919.1	n.890-27631C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74654 AN: 151824 Hom.: 18668 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.492 AC: 74687 AN: 151942 Hom.: 18673 Cov.: 32 AF XY: 0.496 AC XY: 36784 AN XY: 74232

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.479

Alfa AF: 0.514 Hom.: 2519

Bravo AF: 0.489

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1964033; hg19: chr4-132586858;