rs13135284

Variant names:

• chr4-153943598-T-C
• rs13135284
• ENST00000839747.1:n.624-5223T>C

Variant summary

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

The ENST00000839747.1(ENSG00000280241):​n.624-5223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,936 control chromosomes in the GnomAD database, including 34,759 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 (34759 hom., cov: 31)
• Consequence: ENSG00000280241 ENST00000839747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 publications found

Genes affected

ENSG00000280241 (HGNC:58900):

LOC101927947 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839747.1. 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
	ENSG00000280241	ENST00000839747.1		n.624-5223T>C		intron	N/A
	ENSG00000280241	ENST00000839748.1		n.601-5223T>C		intron	N/A
	ENSG00000280241	ENST00000839749.1		n.418-5223T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102116 AN: 151818 Hom.: 34753 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.672 AC: 102171 AN: 151936 Hom.: 34759 Cov.: 31 AF XY: 0.664 AC XY: 49271 AN XY: 74256

African (AFR) AF: 0.608 AC: 25168 AN: 41406

American (AMR) AF: 0.621 AC: 9493 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2195 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3285 AN: 5146

South Asian (SAS) AF: 0.552 AC: 2651 AN: 4804

European-Finnish (FIN) AF: 0.632 AC: 6668 AN: 10550

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50397 AN: 67962

Other (OTH) AF: 0.687 AC: 1450 AN: 2110

Alfa AF: 0.717 Hom.: 171745

Bravo AF: 0.671

Asia WGS AF: 0.582 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.73
DANN	Benign	0.32
PhyloP100		-1.4

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: rs13135284;

hg19: chr4-154864750;