rs2494493

Positions:

• chr1-159840450-A-C

Variant summary

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

The ENST00000645519.1(ENSG00000256029):​n.*1655T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,207,964 control chromosomes in the GnomAD database, including 21,386 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 0.26 (8116 hom., cov: 32)
  • Exomes 𝑓: 0.12 (13270 hom.)
• Consequence: ENSG00000256029 ENST00000645519.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

ENSG00000256029 (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 (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNHG28	NR_147122.1	n.391+676T>G		intron_variant
SNHG28	NR_147123.1	n.226+676T>G		intron_variant
SNHG28	NR_147124.1	n.282-2423T>G		intron_variant
SNHG28	NR_147125.1	n.547+261T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000256029	ENST00000645519.1	n.*1655T>G		non_coding_transcript_exon_variant	9/9			ENSP00000494894.1
SNHG28	ENST00000674949.1	n.603T>G		non_coding_transcript_exon_variant	3/4
SNHG28	ENST00000675503.1	n.586T>G		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39028 AN: 151584 Hom.: 8106 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.235

GnomAD4 exome AF: 0.122 AC: 128450 AN: 1056262 Hom.: 13270 Cov.: 31 AF XY: 0.122 AC XY: 60721 AN XY: 499636

Gnomad4 AFR exome AF: 0.582

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.162

Gnomad4 EAS exome AF: 0.557

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.0935

Gnomad4 OTH exome AF: 0.169

GnomAD4 genome AF: 0.258 AC: 39069 AN: 151702 Hom.: 8116 Cov.: 32 AF XY: 0.258 AC XY: 19157 AN XY: 74130

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.233

Alfa AF: 0.146 Hom.: 1295

Bravo AF: 0.275

Asia WGS AF: 0.415 AC: 1441 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.54

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: rs2494493; hg19: chr1-159810240;