rs9904870

Variant names:

• chr17-76602062-A-C
• rs9904870
• ENST00000701062.1:n.195-11856A>C

Your query was ambiguous. Multiple possible variants found:

• 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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNHG16	ENST00000701062.1	n.195-11856A>C		intron_variant	Intron 2 of 3

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;