16-80889872-T-C

Variant names:

• chr16-80889872-T-C
• rs1981867
• ENST00000650780.1:c.82-59115A>G

Variant summary

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

The ENST00000650780.1(ENSG00000286221):​c.82-59115A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,006 control chromosomes in the GnomAD database, including 41,660 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 0.74 (41660 hom., cov: 31)
• Consequence: ENSG00000286221 ENST00000650780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 8 publications found

Genes affected

ENSG00000286221 (HGNC:):

ARLNC1 (HGNC:53032): (androgen receptor regulated long noncoding RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARLNC1	NR_131947.1	n.92+2633A>G		intron_variant	Intron 1 of 3
ARLNC1	NR_131948.1	n.92+2633A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286221	ENST00000650780.1	c.82-59115A>G		intron_variant	Intron 2 of 2			ENSP00000498782.1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111935 AN: 151888 Hom.: 41610 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.737 AC: 112037 AN: 152006 Hom.: 41660 Cov.: 31 AF XY: 0.737 AC XY: 54764 AN XY: 74294

African (AFR) AF: 0.836 AC: 34651 AN: 41462

American (AMR) AF: 0.767 AC: 11702 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2774 AN: 3472

East Asian (EAS) AF: 0.635 AC: 3288 AN: 5178

South Asian (SAS) AF: 0.617 AC: 2968 AN: 4812

European-Finnish (FIN) AF: 0.682 AC: 7200 AN: 10554

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46920 AN: 67952

Other (OTH) AF: 0.758 AC: 1597 AN: 2106

Alfa AF: 0.715 Hom.: 104411

Bravo AF: 0.751

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1981867; hg19: chr16-80923769;