rs42309

Variant names:

• chr16-9319747-G-T
• rs42309
• ENST00000784364.1:n.90+32495G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000784364.1(LINC02177):​n.90+32495G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,114 control chromosomes in the GnomAD database, including 13,734 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 0.41 (13734 hom., cov: 32)
• Consequence: LINC02177 ENST00000784364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 0 publications found

Genes affected

LINC02177 (HGNC:53039): (long intergenic non-protein coding RNA 2177)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784364.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02177	ENST00000784364.1		n.90+32495G>T		intron	N/A
	LINC02177	ENST00000784365.1		n.85+32495G>T		intron	N/A
	LINC02177	ENST00000784366.1		n.69+32495G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63055 AN: 151996 Hom.: 13739 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.415 AC: 63060 AN: 152114 Hom.: 13734 Cov.: 32 AF XY: 0.414 AC XY: 30752 AN XY: 74338

African (AFR) AF: 0.307 AC: 12754 AN: 41504

American (AMR) AF: 0.371 AC: 5668 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1091 AN: 5170

South Asian (SAS) AF: 0.444 AC: 2135 AN: 4810

European-Finnish (FIN) AF: 0.523 AC: 5530 AN: 10568

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32782 AN: 67994

Other (OTH) AF: 0.410 AC: 866 AN: 2114

Alfa AF: 0.454 Hom.: 3395

Bravo AF: 0.397

Asia WGS AF: 0.317 AC: 1105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.44
DANN	Benign	0.63
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs42309; hg19: chr16-9413604;