4-55730820-T-C

Variant names:

• chr4-55730820-T-C
• rs4333263
• ENST00000767667.1:n.474-4433A>G

Variant summary

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

The ENST00000767667.1(ENSG00000299956):​n.474-4433A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,228 control chromosomes in the GnomAD database, including 54,094 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 0.84 (54094 hom., cov: 32)
• Consequence: ENSG00000299956 ENST00000767667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 0 publications found

Genes affected

ENSG00000299956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299956	ENST00000767667.1	n.474-4433A>G		intron_variant	Intron 4 of 4
ENSG00000299956	ENST00000767668.1	n.485-4433A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127588 AN: 152110 Hom.: 54034 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.839 AC: 127709 AN: 152228 Hom.: 54094 Cov.: 32 AF XY: 0.843 AC XY: 62741 AN XY: 74418

African (AFR) AF: 0.935 AC: 38846 AN: 41538

American (AMR) AF: 0.860 AC: 13152 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2885 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5178 AN: 5186

South Asian (SAS) AF: 0.905 AC: 4370 AN: 4828

European-Finnish (FIN) AF: 0.795 AC: 8414 AN: 10578

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52259 AN: 68012

Other (OTH) AF: 0.842 AC: 1781 AN: 2116

Alfa AF: 0.801 Hom.: 38457

Bravo AF: 0.848

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.54
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4333263; hg19: chr4-56596987;