17-58555182-G-T

Position:

• chr17-58555182-G-T

Variant summary

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

The ENST00000578022.2(SEPTIN4-AS1):​n.637-1627G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,212 control chromosomes in the GnomAD database, including 46,440 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 0.77 (46440 hom., cov: 33)
• Consequence: SEPTIN4-AS1 ENST00000578022.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595

Genes affected

SEPTIN4-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEPTIN4-AS1	NR_110810.1	n.537-1627G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEPTIN4-AS1	ENST00000578022.2	n.637-1627G>T		intron_variant		3
SEPTIN4-AS1	ENST00000580589.5	n.537-1627G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117266 AN: 152094 Hom.: 46370 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.771 AC: 117399 AN: 152212 Hom.: 46440 Cov.: 33 AF XY: 0.776 AC XY: 57716 AN XY: 74396

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.720

Alfa AF: 0.681 Hom.: 50976

Bravo AF: 0.780

Asia WGS AF: 0.932 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9905704; hg19: chr17-56632543;