rs1480931

Variant names:

• chr4-119474654-C-A
• rs1480931
• ENST00000502760.2:n.771+11675C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-119474654-C-A
• chr4-119474654-C-T

Variant summary

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

The ENST00000502760.2(ENSG00000291203):​n.771+11675C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,300 control chromosomes in the GnomAD database, including 5,345 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 0.26 (5345 hom., cov: 31)
• Consequence: ENSG00000291203 ENST00000502760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845
• 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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1	n.727+11675C>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+11675C>A		intron_variant	Intron 6 of 9	3
ENSG00000291203	ENST00000508519.6	n.662+11675C>A		intron_variant	Intron 5 of 10	3
ENSG00000291203	ENST00000510011.6	n.660+11675C>A		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39772 AN: 151196 Hom.: 5341 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.263 AC: 39802 AN: 151300 Hom.: 5345 Cov.: 31 AF XY: 0.262 AC XY: 19301 AN XY: 73802

African (AFR) AF: 0.216 AC: 8906 AN: 41182

American (AMR) AF: 0.263 AC: 3996 AN: 15182

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

East Asian (EAS) AF: 0.384 AC: 1963 AN: 5114

South Asian (SAS) AF: 0.175 AC: 838 AN: 4802

European-Finnish (FIN) AF: 0.257 AC: 2655 AN: 10340

Middle Eastern (MID) AF: 0.213 AC: 61 AN: 286

European-Non Finnish (NFE) AF: 0.293 AC: 19894 AN: 67924

Other (OTH) AF: 0.277 AC: 579 AN: 2094

Alfa AF: 0.259 Hom.: 945

Bravo AF: 0.268

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs1480931; hg19: chr4-120395809;