17-16440456-C-T

Variant names:

• chr17-16440456-C-T
• rs3935801
• ENST00000470491.8:n.448+203C>T

Variant summary

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

The ENST00000470491.8(SNHG29):​n.448+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 ENST00000470491.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 8 publications found

Genes affected

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

ENSG00000266651 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470491.8. 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.231+203C>T		intron	N/A
	SNHG29	NR_027159.1		n.497+203C>T		intron	N/A
	SNHG29	NR_027160.1		n.620+203C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG29	ENST00000470491.8	TSL:1	n.448+203C>T		intron	N/A
	SNHG29	ENST00000475953.6	TSL:1	n.491+203C>T		intron	N/A
	SNHG29	ENST00000481027.5	TSL:1	n.339+203C>T		intron	N/A

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

African (AFR) AF: 0.293 AC: 1488 AN: 5082

American (AMR) AF: 0.311 AC: 2828 AN: 9088

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1826 AN: 4282

East Asian (EAS) AF: 0.221 AC: 1747 AN: 7888

South Asian (SAS) AF: 0.263 AC: 10638 AN: 40444

European-Finnish (FIN) AF: 0.432 AC: 3746 AN: 8680

Middle Eastern (MID) AF: 0.364 AC: 230 AN: 632

European-Non Finnish (NFE) AF: 0.370 AC: 38471 AN: 103868

Other (OTH) AF: 0.361 AC: 3264 AN: 9034

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

African (AFR) AF: 0.293 AC: 12160 AN: 41450

American (AMR) AF: 0.333 AC: 5086 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5174

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4826

European-Finnish (FIN) AF: 0.436 AC: 4605 AN: 10550

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.379 AC: 25785 AN: 67972

Other (OTH) AF: 0.330 AC: 696 AN: 2110

Alfa AF: 0.355 Hom.: 16270

Bravo AF: 0.335

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.92
PhyloP100		0.25

Splicing

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

Other links and lift over

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