14-77763816-A-T

Variant names:

• chr14-77763816-A-T
• rs3759728
• ENST00000556047.1:n.143+2700A>T

Variant summary

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

The ENST00000556047.1(SLIRP-OT1):​n.143+2700A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,124 control chromosomes in the GnomAD database, including 50,985 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 0.82 (50985 hom., cov: 31)
• Consequence: SLIRP-OT1 ENST00000556047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 2 publications found

Genes affected

SLIRP-OT1 (HGNC:26385): (chromosome 14 open reading frame 178)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556047.1. 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
	SLIRP-OT1	NR_161323.1		n.349+2700A>T		intron	N/A
	SLIRP-OT1	NR_161324.1		n.349+2700A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLIRP-OT1	ENST00000556047.1	TSL:1	n.143+2700A>T		intron	N/A
	SLIRP-OT1	ENST00000557011.5	TSL:1	n.143+2700A>T		intron	N/A
	SLIRP-OT1	ENST00000650032.1		n.283+2700A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124277 AN: 152006 Hom.: 50937 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.818 AC: 124381 AN: 152124 Hom.: 50985 Cov.: 31 AF XY: 0.818 AC XY: 60827 AN XY: 74376

African (AFR) AF: 0.791 AC: 32841 AN: 41514

American (AMR) AF: 0.822 AC: 12540 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2894 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3855 AN: 5172

South Asian (SAS) AF: 0.855 AC: 4119 AN: 4818

European-Finnish (FIN) AF: 0.865 AC: 9146 AN: 10578

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56199 AN: 67994

Other (OTH) AF: 0.833 AC: 1762 AN: 2116

Alfa AF: 0.815 Hom.: 6268

Bravo AF: 0.814

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.80
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3759728;

hg19: chr14-78230159;