rs4859315

Variant names:

• chr4-33189747-T-C
• rs4859315
• ENST00000653925.1:n.38-12933T>C

Variant summary

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

The ENST00000653925.1(ENSG00000287968):​n.38-12933T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0856 in 152,234 control chromosomes in the GnomAD database, including 741 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 0.086 (741 hom., cov: 33)
• Consequence: ENSG00000287968 ENST00000653925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 2 publications found

Genes affected

ENSG00000287968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653925.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287968	ENST00000653925.1		n.38-12933T>C		intron	N/A
	ENSG00000287968	ENST00000795184.1		n.419-24622T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13044 AN: 152114 Hom.: 744 Cov.: 33

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0856 AC: 13026 AN: 152234 Hom.: 741 Cov.: 33 AF XY: 0.0901 AC XY: 6703 AN XY: 74430

African (AFR) AF: 0.0238 AC: 990 AN: 41542

American (AMR) AF: 0.0858 AC: 1313 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3470

East Asian (EAS) AF: 0.0941 AC: 487 AN: 5176

South Asian (SAS) AF: 0.0886 AC: 428 AN: 4828

European-Finnish (FIN) AF: 0.175 AC: 1858 AN: 10588

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7263 AN: 68016

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0857 Hom.: 478

Bravo AF: 0.0751

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.83
PhyloP100		-0.86

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4859315;

hg19: chr4-33191369;