5-150617912-G-A

Position:

• chr5-150617912-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000394243.5(SYNPO):​c.-265-191G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0929 in 152,218 control chromosomes in the GnomAD database, including 1,557 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.093 (1557 hom., cov: 33)
• Consequence: SYNPO ENST00000394243.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.126

Genes affected

SYNPO (HGNC:30672): (synaptopodin) Synaptopodin is an actin-associated protein that may play a role in actin-based cell shape and motility. The name synaptopodin derives from the protein's associations with postsynaptic densities and dendritic spines and with renal podocytes (Mundel et al., 1997 [PubMed 9314539]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 5-150617912-G-A is Benign according to our data. Variant chr5-150617912-G-A is described in ClinVar as [Benign]. Clinvar id is 1281397.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNPO	NM_001166208.2	c.-265-191G>A		intron_variant			NP_001159680.1
SYNPO	NM_001166209.2	c.-265-191G>A		intron_variant			NP_001159681.1
SYNPO	XM_006714755.4	c.-265-191G>A		intron_variant			XP_006714818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNPO	ENST00000394243.5	c.-265-191G>A		intron_variant		1		ENSP00000377789	A2
SYNPO	ENST00000522122.1	c.-265-191G>A		intron_variant		2		ENSP00000428378	A2

Frequencies

GnomAD3 genomes AF: 0.0927 AC: 14106 AN: 152100 Hom.: 1549 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0929 AC: 14138 AN: 152218 Hom.: 1557 Cov.: 33 AF XY: 0.0953 AC XY: 7094 AN XY: 74428

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.0346

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.0131

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0570 Hom.: 107

Bravo AF: 0.0991

Asia WGS AF: 0.228 AC: 791 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

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76537501; hg19: chr5-149997474;