rs9904870

Positions:

• chr17-76602062-A-C
• chr17-76602062-A-T

Variant summary

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

The ENST00000701062.1(SNHG16):​n.195-11856A>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 0.14 in 151,854 control chromosomes in the GnomAD database, including 2,764 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 0.14 (2764 hom., cov: 31)
• Consequence: SNHG16 ENST00000701062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

SNHG16 (HGNC:44352): (small nucleolar RNA host gene 16)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNHG16	ENST00000701062.1	n.195-11856A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21153 AN: 151736 Hom.: 2755 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0510

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.140 AC: 21188 AN: 151854 Hom.: 2764 Cov.: 31 AF XY: 0.134 AC XY: 9976 AN XY: 74248

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.0109

Gnomad4 NFE AF: 0.0510

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0394 Hom.: 83

Bravo AF: 0.156

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9904870; hg19: chr17-74598144;