rs892961

Positions:

• chr17-77404018-T-A

Variant summary

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

The NM_001113491.2(SEPTIN9):​c.721+1315T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,958 control chromosomes in the GnomAD database, including 13,532 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 0.41 (13532 hom., cov: 32)
• Consequence: SEPTIN9 NM_001113491.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

SEPTIN9 (HGNC:7323): (septin 9) This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause hereditary neuralgic amyotrophy, also known as neuritis with brachial predilection. A chromosomal translocation involving this gene on chromosome 17 and the MLL gene on chromosome 11 results in acute myelomonocytic leukemia. Multiple alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEPTIN9	NM_001113491.2	c.721+1315T>A		intron_variant		ENST00000427177.6	NP_001106963.1
SEPTIN9	NM_006640.5	c.667+1315T>A		intron_variant		ENST00000329047.13	NP_006631.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEPTIN9	ENST00000329047.13	c.667+1315T>A		intron_variant		1	NM_006640.5	ENSP00000329161	P3
SEPTIN9	ENST00000427177.6	c.721+1315T>A		intron_variant		1	NM_001113491.2	ENSP00000391249	A1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62745 AN: 151840 Hom.: 13506 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.413 AC: 62813 AN: 151958 Hom.: 13532 Cov.: 32 AF XY: 0.405 AC XY: 30085 AN XY: 74256

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.411

Alfa AF: 0.412 Hom.: 1660

Bravo AF: 0.413

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.73

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: rs892961; hg19: chr17-75400100;