rs4866023

Variant names:

• chr5-51049421-A-G
• rs4866023
• ENST00000802600.1:n.164-33859T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-51049421-A-G
• chr5-51049421-A-T

Variant summary

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

The ENST00000802600.1(ENSG00000304338):​n.164-33859T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,008 control chromosomes in the GnomAD database, including 36,063 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 0.67 (36063 hom., cov: 33)
• Consequence: ENSG00000304338 ENST00000802600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 2 publications found

Genes affected

ENSG00000304338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802600.1. 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
	ENSG00000304338	ENST00000802600.1		n.164-33859T>C		intron	N/A
	ENSG00000304338	ENST00000802601.1		n.293+751T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102318 AN: 151890 Hom.: 36008 Cov.: 33

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.674 AC: 102425 AN: 152008 Hom.: 36063 Cov.: 33 AF XY: 0.668 AC XY: 49637 AN XY: 74300

African (AFR) AF: 0.892 AC: 37043 AN: 41550

American (AMR) AF: 0.638 AC: 9733 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2383 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2291 AN: 5162

South Asian (SAS) AF: 0.624 AC: 3010 AN: 4822

European-Finnish (FIN) AF: 0.540 AC: 5692 AN: 10544

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40224 AN: 67908

Other (OTH) AF: 0.671 AC: 1414 AN: 2108

Alfa AF: 0.651 Hom.: 4847

Bravo AF: 0.694

Asia WGS AF: 0.560 AC: 1942 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.088
DANN	Benign	0.51
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4866023; hg19: chr5-50345255; COSMIC: COSV53478433;