chr4-119480680-A-G

Position:

• chr4-119480680-A-G

Variant summary

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

The ENST00000685769.1(ENSG00000291203):​n.1669A>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 ENST00000685769.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

ENSG00000291203 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1	n.728-12653A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291203	ENST00000685769.1	n.1669A>G		non_coding_transcript_exon_variant	7/7
ENSG00000291203	ENST00000693497.1	n.1618A>G		non_coding_transcript_exon_variant	7/7
ENSG00000291203	ENST00000693650.2	n.1552A>G		non_coding_transcript_exon_variant	6/6

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

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.368

Alfa AF: 0.340 Hom.: 9022

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518329; hg19: chr4-120401835;