chr4-130105333-T-C

Variant names:

• chr4-130105333-T-C
• rs114646238
• ENST00000839037.1:n.435-18799T>C

Variant summary

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

The ENST00000839037.1(ENSG00000309145):​n.435-18799T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0461 in 152,208 control chromosomes in the GnomAD database, including 226 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 0.046 (226 hom., cov: 32)
• Consequence: ENSG00000309145 ENST00000839037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 1 publications found

Genes affected

ENSG00000309145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839037.1. 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
	ENSG00000309145	ENST00000839037.1		n.435-18799T>C		intron	N/A
	ENSG00000309145	ENST00000839038.1		n.431+13895T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0461 AC: 7011 AN: 152090 Hom.: 226 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0242

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0461 AC: 7010 AN: 152208 Hom.: 226 Cov.: 32 AF XY: 0.0457 AC XY: 3401 AN XY: 74404

African (AFR) AF: 0.0124 AC: 515 AN: 41576

American (AMR) AF: 0.0241 AC: 369 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.0189 AC: 91 AN: 4820

European-Finnish (FIN) AF: 0.0837 AC: 888 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0732 AC: 4971 AN: 67954

Other (OTH) AF: 0.0275 AC: 58 AN: 2110

Alfa AF: 0.0430 Hom.: 92

Bravo AF: 0.0392

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.29
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs114646238; hg19: chr4-131026488;