rs9993199

Variant names:

• chr4-119471718-G-A
• rs9993199
• ENST00000502760.2:n.771+8739G>A

Variant summary

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

The ENST00000502760.2(ENSG00000291203):​n.771+8739G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,008 control chromosomes in the GnomAD database, including 5,838 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 0.28 (5838 hom., cov: 32)
• Consequence: ENSG00000291203 ENST00000502760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 8 publications found

Genes affected

ENSG00000291203 (HGNC:):

SEPTIN7P14 (HGNC:44219): (septin 7 pseudogene 14)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1	n.727+8739G>A		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291203	ENST00000502760.2	n.771+8739G>A		intron_variant	Intron 6 of 9	3
ENSG00000291203	ENST00000508519.6	n.662+8739G>A		intron_variant	Intron 5 of 10	3
ENSG00000291203	ENST00000510011.6	n.660+8739G>A		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41835 AN: 151890 Hom.: 5830 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.275 AC: 41877 AN: 152008 Hom.: 5838 Cov.: 32 AF XY: 0.273 AC XY: 20277 AN XY: 74302

African (AFR) AF: 0.260 AC: 10789 AN: 41472

American (AMR) AF: 0.268 AC: 4099 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3468

East Asian (EAS) AF: 0.383 AC: 1979 AN: 5164

South Asian (SAS) AF: 0.176 AC: 850 AN: 4822

European-Finnish (FIN) AF: 0.255 AC: 2687 AN: 10550

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19907 AN: 67948

Other (OTH) AF: 0.283 AC: 595 AN: 2106

Alfa AF: 0.275 Hom.: 1042

Bravo AF: 0.283

Asia WGS AF: 0.253 AC: 878 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.69
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs9993199; hg19: chr4-120392873;