4-38276133-A-G

Variant names:

• chr4-38276133-A-G
• rs11725412
• ENST00000757782.1:n.450+270T>C

Variant summary

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

The ENST00000757782.1(ENSG00000287659):​n.450+270T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,198 control chromosomes in the GnomAD database, including 54,823 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 0.83 (54823 hom., cov: 33)
• Consequence: ENSG00000287659 ENST00000757782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 12 publications found

Genes affected

ENSG00000287659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757782.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287659	ENST00000757782.1		n.450+270T>C		intron	N/A
	ENSG00000287659	ENST00000757787.1		n.279+13215T>C		intron	N/A
	ENSG00000287659	ENST00000757788.1		n.318+13215T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126848 AN: 152080 Hom.: 54803 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.834 AC: 126901 AN: 152198 Hom.: 54823 Cov.: 33 AF XY: 0.823 AC XY: 61209 AN XY: 74408

African (AFR) AF: 0.790 AC: 32785 AN: 41482

American (AMR) AF: 0.625 AC: 9549 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3272 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1418 AN: 5170

South Asian (SAS) AF: 0.716 AC: 3457 AN: 4828

European-Finnish (FIN) AF: 0.916 AC: 9710 AN: 10606

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63769 AN: 68038

Other (OTH) AF: 0.839 AC: 1771 AN: 2112

Alfa AF: 0.892 Hom.: 276978

Bravo AF: 0.807

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.80
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11725412; hg19: chr4-38277754;