ENST00000502760.2:n.771+5898A>G

Variant names:

• chr4-119468877-A-G
• rs11098524
• ENST00000502760.2:n.771+5898A>G

Variant summary

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

The ENST00000502760.2(ENSG00000291203):​n.771+5898A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,012 control chromosomes in the GnomAD database, including 5,834 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 (5834 hom., cov: 32)
• Consequence: ENSG00000291203 ENST00000502760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 13 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502760.2. 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
	SEPTIN7P14	NR_037630.1		n.727+5898A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291203	ENST00000502760.2	TSL:3	n.771+5898A>G		intron	N/A
	ENSG00000291203	ENST00000508519.6	TSL:3	n.662+5898A>G		intron	N/A
	ENSG00000291203	ENST00000510011.6	TSL:3	n.660+5898A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41840 AN: 151894 Hom.: 5826 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.206

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: 0.276 AC: 41882 AN: 152012 Hom.: 5834 Cov.: 32 AF XY: 0.273 AC XY: 20280 AN XY: 74320

African (AFR) AF: 0.261 AC: 10818 AN: 41438

American (AMR) AF: 0.268 AC: 4086 AN: 15260

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

East Asian (EAS) AF: 0.383 AC: 1980 AN: 5166

South Asian (SAS) AF: 0.175 AC: 842 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2680 AN: 10568

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19909 AN: 67978

Other (OTH) AF: 0.282 AC: 596 AN: 2112

Alfa AF: 0.281 Hom.: 13604

Bravo AF: 0.283

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		-0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs11098524; hg19: chr4-120390032;