rs9889631

Variant names:

• chr17-58552998-G-T
• rs9889631
• ENST00000578022.2:n.637-3811G>T

Variant summary

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

The ENST00000578022.2(SEPTIN4-AS1):​n.637-3811G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 151,994 control chromosomes in the GnomAD database, including 2,506 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 0.15 (2506 hom., cov: 31)
• Consequence: SEPTIN4-AS1 ENST00000578022.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 2 publications found

Genes affected

SEPTIN4-AS1 (HGNC:51345): (SEPTIN4 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578022.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEPTIN4-AS1	NR_110810.1		n.537-3811G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEPTIN4-AS1	ENST00000578022.2	TSL:3	n.637-3811G>T		intron	N/A
	SEPTIN4-AS1	ENST00000580589.6	TSL:3	n.539-3811G>T		intron	N/A
	SEPTIN4-AS1	ENST00000717184.1		n.1119-3811G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22121 AN: 151876 Hom.: 2499 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.146 AC: 22158 AN: 151994 Hom.: 2506 Cov.: 31 AF XY: 0.149 AC XY: 11043 AN XY: 74304

African (AFR) AF: 0.287 AC: 11900 AN: 41410

American (AMR) AF: 0.0776 AC: 1187 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1608 AN: 5158

South Asian (SAS) AF: 0.278 AC: 1333 AN: 4802

European-Finnish (FIN) AF: 0.0954 AC: 1008 AN: 10570

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0661 AC: 4495 AN: 67980

Other (OTH) AF: 0.127 AC: 268 AN: 2108

Alfa AF: 0.0920 Hom.: 629

Bravo AF: 0.148

Asia WGS AF: 0.302 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.80
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs9889631; hg19: chr17-56630359;