ENST00000368102.5:n.443-4617C>T

Variant names:

• chr1-159845852-G-A
• rs2501354
• ENST00000368102.5:n.443-4617C>T

Variant summary

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

The ENST00000368102.5(ENSG00000256029):​n.443-4617C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,014 control chromosomes in the GnomAD database, including 29,802 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 0.62 (29802 hom., cov: 32)
• Consequence: ENSG00000256029 ENST00000368102.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 7 publications found

Genes affected

ENSG00000256029 (HGNC:):

SNHG28 (HGNC:27647): (small nucleolar RNA host gene 28) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG28	NR_147122.1	n.282-4617C>T		intron_variant	Intron 1 of 3
SNHG28	NR_147123.1	n.117-4617C>T		intron_variant	Intron 1 of 3
SNHG28	NR_147124.1	n.282-7825C>T		intron_variant	Intron 1 of 2
SNHG28	NR_147125.1	n.282-4617C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256029	ENST00000368102.5	n.443-4617C>T		intron_variant	Intron 2 of 5	2
SNHG28	ENST00000491974.2	n.275-7825C>T		intron_variant	Intron 1 of 2	2
SNHG28	ENST00000621242.2	n.163-4617C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94907 AN: 151896 Hom.: 29795 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.625 AC: 94951 AN: 152014 Hom.: 29802 Cov.: 32 AF XY: 0.624 AC XY: 46382 AN XY: 74288

African (AFR) AF: 0.596 AC: 24688 AN: 41420

American (AMR) AF: 0.680 AC: 10401 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3525 AN: 5162

South Asian (SAS) AF: 0.617 AC: 2972 AN: 4816

European-Finnish (FIN) AF: 0.601 AC: 6353 AN: 10570

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42755 AN: 67972

Other (OTH) AF: 0.614 AC: 1294 AN: 2108

Alfa AF: 0.631 Hom.: 54415

Bravo AF: 0.632

Asia WGS AF: 0.645 AC: 2245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.069
DANN	Benign	0.42
PhyloP100		-0.33
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

Other links and lift over

dbSNP: rs2501354; hg19: chr1-159815642;