4-53933078-T-C

Variant names:

• chr4-53933078-T-C
• rs871606
• ENST00000507166.5:c.1018-341847T>C

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-341847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,050 control chromosomes in the GnomAD database, including 1,722 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 0.14 (1722 hom., cov: 32)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433
• Publications: 33 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-341847T>C		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21342 AN: 151932 Hom.: 1724 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.140 AC: 21350 AN: 152050 Hom.: 1722 Cov.: 32 AF XY: 0.144 AC XY: 10672 AN XY: 74316

African (AFR) AF: 0.187 AC: 7747 AN: 41478

American (AMR) AF: 0.134 AC: 2044 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3472

East Asian (EAS) AF: 0.189 AC: 973 AN: 5150

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4814

European-Finnish (FIN) AF: 0.0877 AC: 928 AN: 10578

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7081 AN: 67984

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.117 Hom.: 4025

Bravo AF: 0.141

Asia WGS AF: 0.218 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.57
PhyloP100		0.43
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: rs871606; hg19: chr4-54799245;