7-63117392-A-G

Variant names:

• chr7-63117392-A-G
• rs6956675
• ENST00000458703.1:n.*109T>C

Variant summary

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

The ENST00000458703.1(SEPTIN14P1):​n.*109T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 227,688 control chromosomes in the GnomAD database, including 72,003 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 0.78 (47024 hom., cov: 32)
  • Exomes 𝑓: 0.81 (24979 hom.)
• Consequence: SEPTIN14P1 ENST00000458703.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.51
• Publications: 11 publications found

Genes affected

SEPTIN14P1 (HGNC:51685): (septin 14 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458703.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEPTIN14P1	ENST00000458703.1	TSL:6	n.*109T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119008 AN: 151940 Hom.: 46970 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.768

GnomAD4 exome AF: 0.812 AC: 61385 AN: 75630 Hom.: 24979 AF XY: 0.810 AC XY: 34602 AN XY: 42724

African (AFR) AF: 0.915 AC: 743 AN: 812

American (AMR) AF: 0.893 AC: 2798 AN: 3132

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 997 AN: 1240

East Asian (EAS) AF: 0.828 AC: 1507 AN: 1820

South Asian (SAS) AF: 0.828 AC: 12317 AN: 14874

European-Finnish (FIN) AF: 0.831 AC: 2949 AN: 3548

Middle Eastern (MID) AF: 0.794 AC: 200 AN: 252

European-Non Finnish (NFE) AF: 0.797 AC: 36835 AN: 46226

Other (OTH) AF: 0.816 AC: 3039 AN: 3726

GnomAD4 genome AF: 0.783 AC: 119119 AN: 152058 Hom.: 47024 Cov.: 32 AF XY: 0.786 AC XY: 58432 AN XY: 74338

African (AFR) AF: 0.882 AC: 36578 AN: 41494

American (AMR) AF: 0.829 AC: 12656 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3468

East Asian (EAS) AF: 0.778 AC: 4021 AN: 5166

South Asian (SAS) AF: 0.763 AC: 3678 AN: 4822

European-Finnish (FIN) AF: 0.775 AC: 8183 AN: 10556

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.722 AC: 49096 AN: 67966

Other (OTH) AF: 0.768 AC: 1624 AN: 2114

Alfa AF: 0.743 Hom.: 112310

Bravo AF: 0.793

Asia WGS AF: 0.786 AC: 2732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.45
PhyloP100		-5.5

Splicing

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

Other links and lift over

dbSNP: rs6956675; hg19: chr7-62577770;