3-52226766-A-G

Variant names:

• chr3-52226766-A-G
• rs5743836
• ENST00000494383.1:c.463-2454T>C

Variant summary

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

The ENST00000494383.1(ENSG00000173366):​c.463-2454T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,042 control chromosomes in the GnomAD database, including 3,669 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 0.19 (3669 hom., cov: 32)
• Consequence: ENSG00000173366 ENST00000494383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 324 publications found

Genes affected

ENSG00000173366 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000494383.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000173366	ENST00000494383.1	TSL:2	c.463-2454T>C		intron	N/A	ENSP00000417517.1
	ENSG00000173366	ENST00000478201.1	TSL:2	n.112-1131T>C		intron	N/A	ENSP00000419980.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28922 AN: 151924 Hom.: 3665 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.191 AC: 28975 AN: 152042 Hom.: 3669 Cov.: 32 AF XY: 0.183 AC XY: 13630 AN XY: 74314

African (AFR) AF: 0.351 AC: 14536 AN: 41444

American (AMR) AF: 0.128 AC: 1953 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3468

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5174

South Asian (SAS) AF: 0.104 AC: 502 AN: 4820

European-Finnish (FIN) AF: 0.0608 AC: 643 AN: 10576

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10167 AN: 67966

Other (OTH) AF: 0.196 AC: 415 AN: 2114

Alfa AF: 0.213 Hom.: 1790

Bravo AF: 0.203

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		0.042
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: rs5743836; hg19: chr3-52260782;