rs13131773

Variant names:

• chr4-183024733-C-T
• rs13131773
• ENST00000664752.1:n.285+4285C>T

Variant summary

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

The ENST00000664752.1(ENSG00000286821):​n.285+4285C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0384 in 152,192 control chromosomes in the GnomAD database, including 151 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 0.038 (151 hom., cov: 32)
• Consequence: ENSG00000286821 ENST00000664752.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 1 publications found

Genes affected

ENSG00000286821 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664752.1. 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
	ENSG00000286821	ENST00000664752.1		n.285+4285C>T		intron	N/A
	ENSG00000286821	ENST00000747076.1		n.202+7096C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5846 AN: 152074 Hom.: 152 Cov.: 32

Gnomad AFR AF: 0.00932

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0384 AC: 5845 AN: 152192 Hom.: 151 Cov.: 32 AF XY: 0.0387 AC XY: 2878 AN XY: 74406

African (AFR) AF: 0.00929 AC: 386 AN: 41538

American (AMR) AF: 0.0407 AC: 622 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00894 AC: 31 AN: 3466

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5172

South Asian (SAS) AF: 0.0189 AC: 91 AN: 4822

European-Finnish (FIN) AF: 0.0709 AC: 750 AN: 10584

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3853 AN: 67998

Other (OTH) AF: 0.0336 AC: 71 AN: 2116

Alfa AF: 0.0504 Hom.: 304

Bravo AF: 0.0351

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.83
PhyloP100		-0.21

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: rs13131773;

hg19: chr4-183945886;