4-153847900-C-T

Variant names:

• chr4-153847900-C-T
• rs1125228
• ENST00000839747.1:n.405+5633C>T

Variant summary

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

The ENST00000839747.1(ENSG00000280241):​n.405+5633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,048 control chromosomes in the GnomAD database, including 4,504 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 0.22 (4504 hom., cov: 32)
• Consequence: ENSG00000280241 ENST00000839747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 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.405+5633C>T		intron	N/A
	ENSG00000280241	ENST00000839748.1		n.505+5633C>T		intron	N/A
	ENSG00000280241	ENST00000839749.1		n.200-36059C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33361 AN: 151930 Hom.: 4501 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.219 AC: 33361 AN: 152048 Hom.: 4504 Cov.: 32 AF XY: 0.224 AC XY: 16627 AN XY: 74302

African (AFR) AF: 0.0915 AC: 3796 AN: 41508

American (AMR) AF: 0.186 AC: 2837 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3472

East Asian (EAS) AF: 0.620 AC: 3197 AN: 5160

South Asian (SAS) AF: 0.287 AC: 1379 AN: 4808

European-Finnish (FIN) AF: 0.301 AC: 3175 AN: 10540

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17466 AN: 67956

Other (OTH) AF: 0.239 AC: 505 AN: 2114

Alfa AF: 0.246 Hom.: 10936

Bravo AF: 0.209

Asia WGS AF: 0.417 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.77
PhyloP100		-0.74

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: rs1125228;

hg19: chr4-154769052;