chr1-209952919-CTTA-C

Position:

• chr1-209952919-CTTA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001146262.4(SYT14):​c.61+168_61+170del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 1,066,946 control chromosomes in the GnomAD database, including 1,440 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.040 (174 hom., cov: 31)
  • Exomes 𝑓: 0.049 (1266 hom.)
• Consequence: SYT14 NM_001146262.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.12

Genes affected

SYT14 (HGNC:23143): (synaptotagmin 14) This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate membrane trafficking in synaptic transmission. The encoded protein is a calcium-independent synaptotagmin. Mutations in this gene are a cause of autosomal recessive spinocerebellar ataxia-11 (SCAR11), and a t(1;3) translocation of this gene has been associated with neurodevelopmental abnormalities. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 4. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-209952919-CTTA-C is Benign according to our data. Variant chr1-209952919-CTTA-C is described in ClinVar as [Benign]. Clinvar id is 1302785.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYT14	NM_001146262.4	c.61+168_61+170del		intron_variant		ENST00000367019.6	NP_001139734.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYT14	ENST00000367019.6	c.61+168_61+170del		intron_variant		1	NM_001146262.4	ENSP00000355986

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6063 AN: 152068 Hom.: 175 Cov.: 31

Gnomad AFR AF: 0.00925

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0403

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0467

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0484

GnomAD4 exome AF: 0.0490 AC: 44841 AN: 914760 Hom.: 1266 AF XY: 0.0480 AC XY: 22410 AN XY: 466544

Gnomad4 AFR exome AF: 0.00748

Gnomad4 AMR exome AF: 0.0314

Gnomad4 ASJ exome AF: 0.0878

Gnomad4 EAS exome AF: 0.0000305

Gnomad4 SAS exome AF: 0.0186

Gnomad4 FIN exome AF: 0.0451

Gnomad4 NFE exome AF: 0.0555

Gnomad4 OTH exome AF: 0.0486

GnomAD4 genome AF: 0.0398 AC: 6055 AN: 152186 Hom.: 174 Cov.: 31 AF XY: 0.0381 AC XY: 2831 AN XY: 74390

Gnomad4 AFR AF: 0.00920

Gnomad4 AMR AF: 0.0401

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.0467

Gnomad4 NFE AF: 0.0591

Gnomad4 OTH AF: 0.0479

Alfa AF: 0.0543 Hom.: 39

Bravo AF: 0.0369

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 26, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs200494206; hg19: chr1-210126264;