rs3935801

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-16440456-C-G
• chr17-16440456-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000470491.8(SNHG29):​n.448+203C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,972 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000053 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNHG29	NR_027158.1	n.231+203C>G		intron_variant	Intron 3 of 3
SNHG29	NR_027159.1	n.497+203C>G		intron_variant	Intron 2 of 3
SNHG29	NR_027160.1	n.620+203C>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG29	ENST00000470491.8	n.448+203C>G		intron_variant	Intron 2 of 2	1
SNHG29	ENST00000475953.6	n.491+203C>G		intron_variant	Intron 3 of 4	1
SNHG29	ENST00000481027.5	n.339+203C>G		intron_variant	Intron 3 of 4	1

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 151972 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000528 AC: 1 AN: 189292 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 103836

African (AFR) AF: 0.00 AC: 0 AN: 5084

American (AMR) AF: 0.00 AC: 0 AN: 9100

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4294

East Asian (EAS) AF: 0.00 AC: 0 AN: 7894

South Asian (SAS) AF: 0.00 AC: 0 AN: 40504

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8692

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 634

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 104040

Other (OTH) AF: 0.000110 AC: 1 AN: 9050

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 151972 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74220

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000242 AC: 1 AN: 41358

American (AMR) AF: 0.00 AC: 0 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67994

Other (OTH) AF: 0.00 AC: 0 AN: 2090

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 16270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.8
DANN	Benign	0.84
PhyloP100		0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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;