chr22-39351666-T-A

Position:

• chr22-39351666-T-A

Variant summary

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

The NM_004711.5(SYNGR1):​c.99+1557T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,188 control chromosomes in the GnomAD database, including 11,487 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 0.37 (11487 hom., cov: 34)
• Consequence: SYNGR1 NM_004711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

SYNGR1 (HGNC:11498): (synaptogyrin 1) This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYNGR1	NM_004711.5	c.99+1557T>A		intron_variant		ENST00000328933.10
SYNGR1	NM_145731.4	c.99+1557T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYNGR1	ENST00000328933.10	c.99+1557T>A		intron_variant		1	NM_004711.5	P1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56913 AN: 152072 Hom.: 11482 Cov.: 34

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.374 AC: 56949 AN: 152188 Hom.: 11487 Cov.: 34 AF XY: 0.380 AC XY: 28235 AN XY: 74392

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.369

Alfa AF: 0.209 Hom.: 454

Bravo AF: 0.383

Asia WGS AF: 0.601 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.44
DANN	Benign	0.59

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: rs909685; hg19: chr22-39747671;