16-77606335-A-G

Position:

• chr16-77606335-A-G

Variant summary

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

The NR_184319.1(LINC02131):​n.196-4202A>G 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 0.0596 in 151,770 control chromosomes in the GnomAD database, including 339 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 0.060 (339 hom., cov: 32)
• Consequence: LINC02131 NR_184319.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

Genes affected

LINC02131 (HGNC:52991): (long intergenic non-protein coding RNA 2131)

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 = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02131	NR_184319.1	n.196-4202A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02131	ENST00000563289.1	n.275-4202A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9038 AN: 151650 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.00773

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0200

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.0256

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0432

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

GnomAD4 genome AF: 0.0596 AC: 9046 AN: 151770 Hom.: 339 Cov.: 32 AF XY: 0.0609 AC XY: 4517 AN XY: 74174

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.0577

Gnomad4 ASJ AF: 0.0200

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0480

Alfa AF: 0.0512 Hom.: 101

Bravo AF: 0.0619

Asia WGS AF: 0.169 AC: 586 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	0.51
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13336488; hg19: chr16-77640232;