chr16-9581389-T-G

Variant names:

• chr16-9581389-T-G
• rs12325410
• ENST00000634367.3:n.622+14799T>G

Variant summary

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

The ENST00000634367.3(LINC02177):​n.622+14799T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,144 control chromosomes in the GnomAD database, including 2,456 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 (2456 hom., cov: 31)
• Consequence: LINC02177 ENST00000634367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 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	ENST00000634367.3	n.622+14799T>G		intron_variant	Intron 4 of 4	5
LINC02177	ENST00000784503.1	n.652+14799T>G		intron_variant	Intron 4 of 4
LINC02177	ENST00000784504.1	n.480+14799T>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25305 AN: 152026 Hom.: 2458 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.166 AC: 25326 AN: 152144 Hom.: 2456 Cov.: 31 AF XY: 0.166 AC XY: 12331 AN XY: 74372

African (AFR) AF: 0.181 AC: 7491 AN: 41484

American (AMR) AF: 0.142 AC: 2164 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 308 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2593 AN: 5168

South Asian (SAS) AF: 0.128 AC: 617 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10590

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10065 AN: 68006

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.160 Hom.: 9232

Bravo AF: 0.172

Asia WGS AF: 0.325 AC: 1130 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	7.5
DANN	Benign	0.71
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs12325410; hg19: chr16-9675246;