rs9889631

Positions:

• chr17-58552998-G-T

Variant summary

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

The NR_110810.1(SEPTIN4-AS1):​n.537-3811G>T variant causes a intron, non coding transcript 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 NR_110810.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEPTIN4-AS1	NR_110810.1	n.537-3811G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEPTIN4-AS1	ENST00000580589.5	n.537-3811G>T		intron_variant, non_coding_transcript_variant		3
SEPTIN4-AS1	ENST00000578022.2	n.637-3811G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.0954

Gnomad4 NFE AF: 0.0661

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0916 Hom.: 559

Bravo AF: 0.148

Asia WGS AF: 0.302 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9889631; hg19: chr17-56630359;