17-16439499-T-C

Variant names:

• chr17-16439499-T-C
• rs4072454
• ENST00000470491.8:n.379+85T>C

Variant summary

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

The ENST00000480811.6(SNHG29):​n.197T>C 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 0.344 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 ENST00000480811.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.04
• Publications: 10 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000480811.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG29	NR_027158.1		n.162+85T>C		intron	N/A
	SNHG29	NR_027159.1		n.428+85T>C		intron	N/A
	SNHG29	NR_027160.1		n.429-82T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG29	ENST00000470491.8	TSL:1	n.379+85T>C		intron	N/A
	SNHG29	ENST00000475953.6	TSL:1	n.378+85T>C		intron	N/A
	SNHG29	ENST00000481027.5	TSL:1	n.95-29T>C		intron	N/A

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

GnomAD2 exomes AF: 0.335 AC: 83851 AN: 250602 AF XY: 0.334

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 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

African (AFR) AF: 0.288 AC: 3025 AN: 10496

American (AMR) AF: 0.293 AC: 10639 AN: 36290

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 5052 AN: 11740

East Asian (EAS) AF: 0.224 AC: 2947 AN: 13160

South Asian (SAS) AF: 0.261 AC: 17393 AN: 66758

European-Finnish (FIN) AF: 0.431 AC: 13783 AN: 31946

Middle Eastern (MID) AF: 0.353 AC: 1007 AN: 2854

European-Non Finnish (NFE) AF: 0.371 AC: 71018 AN: 191492

Other (OTH) AF: 0.353 AC: 5884 AN: 16670

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

African (AFR) AF: 0.290 AC: 12058 AN: 41510

American (AMR) AF: 0.333 AC: 5089 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1579 AN: 3464

East Asian (EAS) AF: 0.232 AC: 1204 AN: 5180

South Asian (SAS) AF: 0.255 AC: 1232 AN: 4828

European-Finnish (FIN) AF: 0.436 AC: 4613 AN: 10586

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25793 AN: 67990

Other (OTH) AF: 0.330 AC: 697 AN: 2114

Alfa AF: 0.373 Hom.: 2419

Bravo AF: 0.334

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.19
DANN	Benign	0.48
PhyloP100		-4.0
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

Other links and lift over

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