rs17099207

chr14-61762395-G-A

Variant summary

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

The 14-61762395-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,563,608 control chromosomes in the GnomAD database, including 66,687 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 0.32 (7976 hom., cov: 32)
  • Exomes 𝑓: 0.28 (58711 hom.)
• Consequence: SNAPC1 NM_003082.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

Genes affected

SNAPC1 (HGNC:11134): (small nuclear RNA activating complex polypeptide 1) Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNAPC1	NM_003082.4			upstream_gene_variant		ENST00000216294.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAPC1	ENST00000216294.5			upstream_gene_variant		1	NM_003082.4	P1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48059 AN: 151168 Hom.: 7942 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.331

GnomAD4 exome AF: 0.284 AC: 401103 AN: 1412320 Hom.: 58711 Cov.: 31 AF XY: 0.286 AC XY: 200920 AN XY: 701722

Gnomad4 AFR exome AF: 0.380

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.267

Gnomad4 EAS exome AF: 0.206

Gnomad4 SAS exome AF: 0.382

Gnomad4 FIN exome AF: 0.271

Gnomad4 NFE exome AF: 0.273

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.318 AC: 48136 AN: 151288 Hom.: 7976 Cov.: 32 AF XY: 0.320 AC XY: 23678 AN XY: 73894

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.330

Alfa AF: 0.306 Hom.: 919

Bravo AF: 0.327

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	6.9
Dann	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17099207; hg19: chr14-62229113; COSMIC: COSV53519972;