7-35909708-T-C

Variant names:

• chr7-35909708-T-C
• rs6980161
• ENST00000728890.1:n.149+928T>C

Variant summary

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

The ENST00000728890.1(ENSG00000295259):​n.149+928T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 152,264 control chromosomes in the GnomAD database, including 68,217 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 0.94 (68217 hom., cov: 32)
• Consequence: ENSG00000295259 ENST00000728890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 1 publications found

Genes affected

ENSG00000295259 (HGNC:):

SEPTIN7 (HGNC:1717): (septin 7) This gene encodes a protein that is highly similar to the CDC10 protein of Saccharomyces cerevisiae. The protein also shares similarity with Diff 6 of Drosophila and with H5 of mouse. Each of these similar proteins, including the yeast CDC10, contains a GTP-binding motif. The yeast CDC10 protein is a structural component of the 10 nm filament which lies inside the cytoplasmic membrane and is essential for cytokinesis. This human protein functions in gliomagenesis and in the suppression of glioma cell growth, and it is required for the association of centromere-associated protein E with the kinetochore. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified on chromosomes 5, 7, 9, 10, 11, 14, 17 and 19. [provided by RefSeq, Jul 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN7	XM_011515656.3	c.1168-2943T>C		intron_variant	Intron 12 of 14		XP_011513958.1
SEPTIN7	XM_011515661.3	c.1168-2943T>C		intron_variant	Intron 12 of 13		XP_011513963.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295259	ENST00000728890.1	n.149+928T>C		intron_variant	Intron 2 of 5
ENSG00000295259	ENST00000728891.1	n.177+928T>C		intron_variant	Intron 1 of 4
ENSG00000295259	ENST00000728892.1	n.184+928T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143558 AN: 152146 Hom.: 68199 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.943 AC: 143628 AN: 152264 Hom.: 68217 Cov.: 32 AF XY: 0.945 AC XY: 70345 AN XY: 74448

African (AFR) AF: 0.817 AC: 33904 AN: 41500

American (AMR) AF: 0.979 AC: 14979 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3442 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5178 AN: 5182

South Asian (SAS) AF: 0.989 AC: 4774 AN: 4828

European-Finnish (FIN) AF: 0.982 AC: 10418 AN: 10614

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67723 AN: 68044

Other (OTH) AF: 0.954 AC: 2018 AN: 2116

Alfa AF: 0.976 Hom.: 212081

Bravo AF: 0.936

Asia WGS AF: 0.977 AC: 3398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.37
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6980161; hg19: chr7-35949318;