17-16439499-T-C

Position:

• chr17-16439499-T-C

Variant summary

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

The NR_027171.1(SNHG29):​n.428+85T>C 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 0.344 in 533,562 control chromosomes in the GnomAD database, including 33,020 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 0.35 (9503 hom., cov: 33)
  • Exomes 𝑓: 0.34 (23517 hom.)
• Consequence: SNHG29 NR_027171.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04

Genes affected

SNHG29 (HGNC:28619): (small nucleolar RNA host gene 29)

SNORD49B (HGNC:32721): (small nucleolar RNA, C/D box 49B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNHG29	NR_027171.1	n.428+85T>C		intron_variant, non_coding_transcript_variant
SNORD49B	NR_003043.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG29	ENST00000702366.1	n.112+85T>C		intron_variant, non_coding_transcript_variant
SNORD49B	ENST00000365172.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52575 AN: 152038 Hom.: 9496 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.328

GnomAD3 exomes AF: 0.335 AC: 83851 AN: 250602 Hom.: 14715 AF XY: 0.334 AC XY: 45361 AN XY: 135700

Gnomad AFR exome AF: 0.283

Gnomad AMR exome AF: 0.294

Gnomad ASJ exome AF: 0.433

Gnomad EAS exome AF: 0.225

Gnomad SAS exome AF: 0.251

Gnomad FIN exome AF: 0.432

Gnomad NFE exome AF: 0.366

Gnomad OTH exome AF: 0.355

GnomAD4 exome AF: 0.343 AC: 130748 AN: 381406 Hom.: 23517 Cov.: 0 AF XY: 0.338 AC XY: 73426 AN XY: 217050

Gnomad4 AFR exome AF: 0.288

Gnomad4 AMR exome AF: 0.293

Gnomad4 ASJ exome AF: 0.430

Gnomad4 EAS exome AF: 0.224

Gnomad4 SAS exome AF: 0.261

Gnomad4 FIN exome AF: 0.431

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.353

GnomAD4 genome AF: 0.346 AC: 52609 AN: 152156 Hom.: 9503 Cov.: 33 AF XY: 0.346 AC XY: 25725 AN XY: 74402

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.330

Alfa AF: 0.375 Hom.: 2384

Bravo AF: 0.334

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.19
DANN	Benign	0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4072454; hg19: chr17-16342813; COSMIC: COSV58428414;