rs79356259

Variant names:

• chr17-37516711-C-T
• rs79356259
• NM_007247.6:c.*2229G>A

Variant summary

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

The NM_007247.6(SYNRG):​c.*2229G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 150,476 control chromosomes in the GnomAD database, including 816 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 0.097 (816 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SYNRG NM_007247.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 5 publications found

Genes affected

SYNRG (HGNC:557): (synergin gamma) This gene encodes a protein that interacts with the gamma subunit of AP1 clathrin-adaptor complex. The AP1 complex is located at the trans-Golgi network and associates specific proteins with clathrin-coated vesicles. This encoded protein may act to connect the AP1 complex to other proteins. Alternatively spliced transcript variants that encode different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007247.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYNRG	NM_007247.6	MANE Select	c.*2229G>A		3_prime_UTR	Exon 22 of 22	NP_009178.3
	SYNRG	NM_001405103.1		c.*2229G>A		3_prime_UTR	Exon 24 of 24	NP_001392032.1
	SYNRG	NM_198882.3		c.*2229G>A		3_prime_UTR	Exon 22 of 22	NP_942583.1	Q9UMZ2-7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYNRG	ENST00000612223.5	TSL:1 MANE Select	c.*2229G>A		3_prime_UTR	Exon 22 of 22	ENSP00000483453.1	Q9UMZ2-1
	SYNRG	ENST00000936284.1		c.*2229G>A		3_prime_UTR	Exon 23 of 23	ENSP00000606343.1
	SYNRG	ENST00000864289.1		c.*2229G>A		3_prime_UTR	Exon 21 of 21	ENSP00000534348.1

Frequencies

GnomAD3 genomes AF: 0.0973 AC: 14629 AN: 150364 Hom.: 814 Cov.: 30

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.0940

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.110

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0972 AC: 14626 AN: 150476 Hom.: 816 Cov.: 30 AF XY: 0.0977 AC XY: 7164 AN XY: 73294

African (AFR) AF: 0.0493 AC: 2014 AN: 40866

American (AMR) AF: 0.104 AC: 1572 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 299 AN: 3456

East Asian (EAS) AF: 0.177 AC: 906 AN: 5112

South Asian (SAS) AF: 0.131 AC: 625 AN: 4764

European-Finnish (FIN) AF: 0.0880 AC: 891 AN: 10130

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 7970 AN: 67750

Other (OTH) AF: 0.110 AC: 230 AN: 2094

Alfa AF: 0.0994 Hom.: 106

Bravo AF: 0.0979

Asia WGS AF: 0.148 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.89
PhyloP100		-1.7
Mutation Taster		=100/0	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: rs79356259; hg19: chr17-35876814;