rs17550532

Variant names:

• chr16-9650238-A-G
• rs17550532
• ENST00000784503.1:n.653-5213A>G

Variant summary

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

The ENST00000784503.1(LINC02177):​n.653-5213A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,170 control chromosomes in the GnomAD database, including 2,433 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 0.17 (2433 hom., cov: 32)
• Consequence: LINC02177 ENST00000784503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02177	ENST00000784503.1	n.653-5213A>G		intron_variant	Intron 4 of 4
LINC02177	ENST00000784504.1	n.481-5213A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25929 AN: 152052 Hom.: 2435 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.170 AC: 25934 AN: 152170 Hom.: 2433 Cov.: 32 AF XY: 0.167 AC XY: 12390 AN XY: 74406

African (AFR) AF: 0.125 AC: 5192 AN: 41510

American (AMR) AF: 0.166 AC: 2538 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3470

East Asian (EAS) AF: 0.0783 AC: 406 AN: 5182

South Asian (SAS) AF: 0.164 AC: 788 AN: 4816

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10596

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14106 AN: 67994

Other (OTH) AF: 0.204 AC: 429 AN: 2106

Alfa AF: 0.196 Hom.: 10328

Bravo AF: 0.167

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs17550532; hg19: chr16-9744095;