rs2389803

Variant names:

• chr4-119472356-G-A
• rs2389803
• ENST00000502760.2:n.771+9377G>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+9377G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,812 control chromosomes in the GnomAD database, including 6,464 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 0.29 (6464 hom., cov: 31)
• Consequence: ENSG00000291203 ENST00000502760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.737
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1	n.727+9377G>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+9377G>A		intron_variant	Intron 6 of 9	3
ENSG00000291203	ENST00000508519.6	n.662+9377G>A		intron_variant	Intron 5 of 10	3
ENSG00000291203	ENST00000510011.6	n.660+9377G>A		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43997 AN: 151694 Hom.: 6456 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.290 AC: 44041 AN: 151812 Hom.: 6464 Cov.: 31 AF XY: 0.287 AC XY: 21317 AN XY: 74200

African (AFR) AF: 0.312 AC: 12909 AN: 41386

American (AMR) AF: 0.273 AC: 4170 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3464

East Asian (EAS) AF: 0.381 AC: 1950 AN: 5114

South Asian (SAS) AF: 0.177 AC: 849 AN: 4810

European-Finnish (FIN) AF: 0.253 AC: 2669 AN: 10548

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19906 AN: 67924

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.283 Hom.: 1113

Bravo AF: 0.300

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.33
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs2389803; hg19: chr4-120393511;