4-119489452-A-C

Position:

• chr4-119489452-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502760.2(ENSG00000291203):​n.772-3881A>C variant causes a intron 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 ENST00000502760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

ENSG00000291203 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1	n.728-3881A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291203	ENST00000498873.5	n.75+735A>C		intron_variant		5
ENSG00000291203	ENST00000502760.2	n.772-3881A>C		intron_variant		3
ENSG00000291203	ENST00000508519.6	n.735+735A>C		intron_variant		3

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

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.282

Alfa AF: 0.275 Hom.: 1016

Bravo AF: 0.283

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12508504; hg19: chr4-120410607;