rs6659742

Variant names:

• chr1-159848723-C-T
• rs6659742
• ENST00000368102.5:n.442+6034G>A

Variant summary

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

The ENST00000368102.5(ENSG00000256029):​n.442+6034G>A variant causes a intron 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: ENSG00000256029 ENST00000368102.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 14 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=-0.84).
• 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 rank	MANE	Protein	UniProt
SNHG28	NR_147122.1	n.281+6034G>A		intron_variant	Intron 1 of 3
SNHG28	NR_147123.1	n.116+6199G>A		intron_variant	Intron 1 of 3
SNHG28	NR_147124.1	n.281+6034G>A		intron_variant	Intron 1 of 2
SNHG28	NR_147125.1	n.281+6034G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256029	ENST00000368102.5	n.442+6034G>A		intron_variant	Intron 2 of 5	2
SNHG28	ENST00000491974.2	n.274+6034G>A		intron_variant	Intron 1 of 2	2
SNHG28	ENST00000621242.2	n.162+6036G>A		intron_variant	Intron 1 of 3	5

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

African (AFR) AF: 0.369 AC: 15283 AN: 41410

American (AMR) AF: 0.459 AC: 6999 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5166

South Asian (SAS) AF: 0.374 AC: 1802 AN: 4816

European-Finnish (FIN) AF: 0.379 AC: 3992 AN: 10534

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27257 AN: 67962

Other (OTH) AF: 0.377 AC: 796 AN: 2112

Alfa AF: 0.401 Hom.: 23493

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
PhyloP100		2.0
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: rs6659742; hg19: chr1-159818513;