rs30524

Variant names:

• chr5-132775238-A-C
• rs30524
• NM_001098811.2:c.30+1870T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-132775238-A-C
• chr5-132775238-A-G
• chr5-132775238-A-T

Variant summary

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

The NM_001098811.2(SEPTIN8):​c.30+1870T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,130 control chromosomes in the GnomAD database, including 16,856 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 0.36 (16856 hom., cov: 33)
• Consequence: SEPTIN8 NM_001098811.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 5 publications found

Genes affected

SEPTIN8 (HGNC:16511): (septin 8) This gene is a member of the septin family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse, and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN8	NM_001098811.2	c.30+1870T>G		intron_variant	Intron 1 of 9	ENST00000378719.7	NP_001092281.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEPTIN8	ENST00000378719.7	c.30+1870T>G		intron_variant	Intron 1 of 9	1	NM_001098811.2	ENSP00000367991.2

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55111 AN: 152012 Hom.: 16811 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.363 AC: 55224 AN: 152130 Hom.: 16856 Cov.: 33 AF XY: 0.368 AC XY: 27334 AN XY: 74374

African (AFR) AF: 0.802 AC: 33266 AN: 41480

American (AMR) AF: 0.299 AC: 4579 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3846 AN: 5182

South Asian (SAS) AF: 0.165 AC: 795 AN: 4828

European-Finnish (FIN) AF: 0.291 AC: 3079 AN: 10586

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8470 AN: 67982

Other (OTH) AF: 0.298 AC: 628 AN: 2106

Alfa AF: 0.0919 Hom.: 138

Bravo AF: 0.391

Asia WGS AF: 0.430 AC: 1498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.5
DANN	Benign	0.80
PhyloP100		0.59
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: rs30524; hg19: chr5-132110930;