4-119489452-A-C

Variant names:

• chr4-119489452-A-C
• rs12508504
• ENST00000776175.1:n.1472A>C

Variant summary

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

The ENST00000776175.1(ENSG00000291203):​n.1472A>C 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 0.275 in 151,920 control chromosomes in the GnomAD database, including 5,831 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 (5831 hom., cov: 32)
• Consequence: ENSG00000291203 ENST00000776175.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 8 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=-1.03).
• 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: ENST00000776175.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEPTIN7P14	NR_037630.1		n.728-3881A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291203	ENST00000776175.1		n.1472A>C		non_coding_transcript_exon	Exon 6 of 6
	ENSG00000291203	ENST00000776176.1		n.1339A>C		non_coding_transcript_exon	Exon 6 of 6
	ENSG00000291203	ENST00000498873.5	TSL:5	n.75+735A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41768 AN: 151802 Hom.: 5823 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.177

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: 0.275 AC: 41812 AN: 151920 Hom.: 5831 Cov.: 32 AF XY: 0.272 AC XY: 20223 AN XY: 74226

African (AFR) AF: 0.260 AC: 10779 AN: 41454

American (AMR) AF: 0.268 AC: 4079 AN: 15240

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

East Asian (EAS) AF: 0.383 AC: 1962 AN: 5122

South Asian (SAS) AF: 0.176 AC: 851 AN: 4824

European-Finnish (FIN) AF: 0.254 AC: 2681 AN: 10568

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

European-Non Finnish (NFE) AF: 0.293 AC: 19893 AN: 67930

Other (OTH) AF: 0.282 AC: 595 AN: 2110

Alfa AF: 0.274 Hom.: 1043

Bravo AF: 0.283

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12508504; hg19: chr4-120410607;