rs17099207

Variant names:

• chr14-61762395-G-A
• rs17099207
• ENST00000555937.1:n.149-4481G>A

Variant summary

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

The ENST00000555937.1(ENSG00000258964):​n.149-4481G>A variant causes a intron 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: ENSG00000258964 ENST00000555937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 10 publications found

Genes affected

ENSG00000258964 (HGNC:):

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555937.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAPC1	NM_003082.4	MANE Select	c.-66G>A		upstream_gene	N/A	NP_003073.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258964	ENST00000555937.1	TSL:4	n.149-4481G>A		intron	N/A
	SNAPC1	ENST00000216294.5	TSL:1 MANE Select	c.-66G>A		upstream_gene	N/A	ENSP00000216294.4

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

African (AFR) AF: 0.380 AC: 12170 AN: 32068

American (AMR) AF: 0.367 AC: 13702 AN: 37332

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 6727 AN: 25174

East Asian (EAS) AF: 0.206 AC: 7656 AN: 37112

South Asian (SAS) AF: 0.382 AC: 31500 AN: 82364

European-Finnish (FIN) AF: 0.271 AC: 10727 AN: 39624

Middle Eastern (MID) AF: 0.319 AC: 1330 AN: 4164

European-Non Finnish (NFE) AF: 0.273 AC: 299708 AN: 1095904

Other (OTH) AF: 0.300 AC: 17583 AN: 58578

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

African (AFR) AF: 0.382 AC: 15750 AN: 41256

American (AMR) AF: 0.368 AC: 5612 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3464

East Asian (EAS) AF: 0.231 AC: 1148 AN: 4974

South Asian (SAS) AF: 0.390 AC: 1856 AN: 4756

European-Finnish (FIN) AF: 0.262 AC: 2761 AN: 10544

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 18981 AN: 67764

Other (OTH) AF: 0.330 AC: 692 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.9
DANN	Benign	0.87
PhyloP100		0.034
PromoterAI		0.60	Over-expression
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

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