rs67343076

Positions:

• chr16-84930984-G-A

Variant summary

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

The ENST00000569104.1(LINC02176):​n.253+2379G>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 0.192 in 151,342 control chromosomes in the GnomAD database, including 3,212 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 0.19 (3212 hom., cov: 31)
• Consequence: LINC02176 ENST00000569104.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962

Genes affected

LINC02176 (HGNC:53038): (long intergenic non-protein coding RNA 2176)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02176	XR_933830.2	n.631+2379G>A		intron_variant, non_coding_transcript_variant
LINC02176	XR_933832.3	n.631+2379G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02176	ENST00000569104.1	n.253+2379G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29043 AN: 151224 Hom.: 3213 Cov.: 31

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.192 AC: 29043 AN: 151342 Hom.: 3212 Cov.: 31 AF XY: 0.199 AC XY: 14693 AN XY: 73918

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.192

Alfa AF: 0.204 Hom.: 455

Bravo AF: 0.174

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67343076; hg19: chr16-84964590;