4-53868171-C-G

Variant names:

• chr4-53868171-C-G
• rs1391759
• ENST00000507166.5:c.1018-406754C>G

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-406754C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,070 control chromosomes in the GnomAD database, including 55,141 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 0.84 (55141 hom., cov: 31)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 1 publications found

Genes affected

ENSG00000282278 (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 (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507166.5. 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
	ENSG00000282278	ENST00000507166.5	TSL:2	c.1018-406754C>G		intron	N/A	ENSP00000423325.1	A0A0B4J203

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128077 AN: 151952 Hom.: 55108 Cov.: 31

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.843 AC: 128159 AN: 152070 Hom.: 55141 Cov.: 31 AF XY: 0.847 AC XY: 63004 AN XY: 74368

African (AFR) AF: 0.643 AC: 26626 AN: 41396

American (AMR) AF: 0.916 AC: 14001 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3081 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5054 AN: 5164

South Asian (SAS) AF: 0.899 AC: 4333 AN: 4822

European-Finnish (FIN) AF: 0.968 AC: 10267 AN: 10602

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62033 AN: 68010

Other (OTH) AF: 0.862 AC: 1825 AN: 2116

Alfa AF: 0.872 Hom.: 3004

Bravo AF: 0.832

Asia WGS AF: 0.928 AC: 3225 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	4.3
DANN	Benign	0.56
PhyloP100		-0.032
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1391759; hg19: chr4-54734338;