rs2501354

Positions:

• chr1-159845852-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147123.1(SNHG28):​n.117-4617C>T variant causes a intron, non coding transcript 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: SNHG28 NR_147123.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SNHG28	NR_147123.1	n.117-4617C>T		intron_variant, non_coding_transcript_variant
SNHG28	NR_147122.1	n.282-4617C>T		intron_variant, non_coding_transcript_variant
SNHG28	NR_147124.1	n.282-7825C>T		intron_variant, non_coding_transcript_variant
SNHG28	NR_147125.1	n.282-4617C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG28	ENST00000676072.1	n.151-3538C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.614

Alfa AF: 0.632 Hom.: 39980

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2501354; hg19: chr1-159815642;