rs4933583

Variant names:

• chr10-90269182-C-A
• rs4933583
• ENST00000749546.1:n.228-766G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-90269182-C-A
• chr10-90269182-C-G

Variant summary

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

The ENST00000749546.1(ENSG00000297645):​n.228-766G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,962 control chromosomes in the GnomAD database, including 6,892 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 0.29 (6892 hom., cov: 32)
• Consequence: ENSG00000297645 ENST00000749546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 2 publications found

Genes affected

ENSG00000297645 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000749546.1. 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
	ENSG00000297645	ENST00000749546.1		n.228-766G>T		intron	N/A
	ENSG00000297655	ENST00000749800.1		n.67+19644G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43788 AN: 151844 Hom.: 6874 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.288 AC: 43835 AN: 151962 Hom.: 6892 Cov.: 32 AF XY: 0.295 AC XY: 21874 AN XY: 74262

African (AFR) AF: 0.197 AC: 8158 AN: 41506

American (AMR) AF: 0.398 AC: 6066 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2313 AN: 5134

South Asian (SAS) AF: 0.156 AC: 748 AN: 4806

European-Finnish (FIN) AF: 0.460 AC: 4855 AN: 10558

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19954 AN: 67928

Other (OTH) AF: 0.281 AC: 593 AN: 2112

Alfa AF: 0.297 Hom.: 841

Bravo AF: 0.288

Asia WGS AF: 0.283 AC: 981 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.75
PhyloP100		0.57

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: rs4933583;

hg19: chr10-92028939;