chr17-16440456-C-T

Position:

• chr17-16440456-C-T

Variant summary

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

The ENST00000470491.7(SNHG29):​n.447+203C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 341,030 control chromosomes in the GnomAD database, including 21,005 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 (9525 hom., cov: 32)
  • Exomes 𝑓: 0.34 (11480 hom.)
• Consequence: SNHG29 ENST00000470491.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

Genes affected

SNHG29 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• 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_027158.1	n.231+203C>T		intron_variant
SNHG29	NR_027159.1	n.497+203C>T		intron_variant
SNHG29	NR_027160.1	n.620+203C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG29	ENST00000470491.7	n.447+203C>T		intron_variant		1
SNHG29	ENST00000475953.6	n.491+203C>T		intron_variant		1
SNHG29	ENST00000481027.5	n.339+203C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52636 AN: 151914 Hom.: 9518 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.329

GnomAD4 exome AF: 0.340 AC: 64238 AN: 188998 Hom.: 11480 Cov.: 0 AF XY: 0.330 AC XY: 34248 AN XY: 103670

Gnomad4 AFR exome AF: 0.293

Gnomad4 AMR exome AF: 0.311

Gnomad4 ASJ exome AF: 0.426

Gnomad4 EAS exome AF: 0.221

Gnomad4 SAS exome AF: 0.263

Gnomad4 FIN exome AF: 0.432

Gnomad4 NFE exome AF: 0.370

Gnomad4 OTH exome AF: 0.361

GnomAD4 genome AF: 0.346 AC: 52670 AN: 152032 Hom.: 9525 Cov.: 32 AF XY: 0.346 AC XY: 25739 AN XY: 74322

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.330

Alfa AF: 0.355 Hom.: 12919

Bravo AF: 0.335

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3935801; hg19: chr17-16343770; COSMIC: COSV58430196;