rs6659742

chr1-159848723-C-T

Variant summary

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

The NR_147123.1(SNHG28):n.116+6199G>A 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 0.39 in 151,924 control chromosomes in the GnomAD database, including 11,701 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 0.39 (11701 hom., cov: 31)
• Consequence: SNHG28 NR_147123.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNHG28	NR_147123.1	n.116+6199G>A		intron_variant, non_coding_transcript_variant
SNHG28	NR_147122.1	n.281+6034G>A		intron_variant, non_coding_transcript_variant
SNHG28	NR_147124.1	n.281+6034G>A		intron_variant, non_coding_transcript_variant
SNHG28	NR_147125.1	n.281+6034G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG28	ENST00000676072.1	n.150+6199G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59247 AN: 151806 Hom.: 11686 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.390 AC: 59295 AN: 151924 Hom.: 11701 Cov.: 31 AF XY: 0.391 AC XY: 29044 AN XY: 74266

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.377

Alfa AF: 0.402 Hom.: 16191

Bravo AF: 0.395

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	13
Dann	Benign	0.78

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: rs6659742; hg19: chr1-159818513;