rs10518329

Variant names:

• chr4-119480680-A-G
• rs10518329
• ENST00000685769.2:n.1704A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-119480680-A-G
• chr4-119480680-A-T

Variant summary

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

The ENST00000685769.2(ENSG00000291203):​n.1704A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,944 control chromosomes in the GnomAD database, including 12,165 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 0.39 (12165 hom., cov: 32)
• Consequence: ENSG00000291203 ENST00000685769.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 18 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1	n.728-12653A>G		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291203	ENST00000685769.2	n.1704A>G		non_coding_transcript_exon_variant	Exon 7 of 7
ENSG00000291203	ENST00000693497.2	n.1626A>G		non_coding_transcript_exon_variant	Exon 7 of 7
ENSG00000291203	ENST00000693650.3	n.1581A>G		non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58474 AN: 151826 Hom.: 12129 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.385 AC: 58561 AN: 151944 Hom.: 12165 Cov.: 32 AF XY: 0.382 AC XY: 28389 AN XY: 74252

African (AFR) AF: 0.548 AC: 22698 AN: 41448

American (AMR) AF: 0.323 AC: 4931 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2216 AN: 5142

South Asian (SAS) AF: 0.243 AC: 1172 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3366 AN: 10582

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22319 AN: 67924

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.349 Hom.: 12430

Bravo AF: 0.402

Asia WGS AF: 0.326 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.71
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10518329; hg19: chr4-120401835;