rs4699052

Variant names:

• chr4-103216633-C-T
• rs4699052
• ENST00000828663.1:n.93-5888G>A

Variant summary

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

The ENST00000828663.1(ENSG00000307755):​n.93-5888G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,872 control chromosomes in the GnomAD database, including 14,704 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 0.44 (14704 hom., cov: 32)
• Consequence: ENSG00000307755 ENST00000828663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 26 publications found

Genes affected

ENSG00000307755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 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
ENSG00000307755	ENST00000828663.1	n.93-5888G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66054 AN: 151752 Hom.: 14681 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.435 AC: 66129 AN: 151872 Hom.: 14704 Cov.: 32 AF XY: 0.437 AC XY: 32422 AN XY: 74244

African (AFR) AF: 0.531 AC: 21974 AN: 41410

American (AMR) AF: 0.407 AC: 6212 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1946 AN: 5172

South Asian (SAS) AF: 0.445 AC: 2148 AN: 4824

European-Finnish (FIN) AF: 0.416 AC: 4375 AN: 10520

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26529 AN: 67916

Other (OTH) AF: 0.452 AC: 950 AN: 2100

Alfa AF: 0.406 Hom.: 56435

Bravo AF: 0.439

Asia WGS AF: 0.411 AC: 1430 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.32
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs4699052; hg19: chr4-104137790;