chr3-52226766-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000173366 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000173366	ENST00000494383.1	c.463-2454T>C		intron_variant	Intron 4 of 4	2		ENSP00000417517.1
ENSG00000173366	ENST00000478201.1	n.112-1131T>C		intron_variant	Intron 1 of 2	2		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

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.00445

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.196

Alfa AF: 0.196 Hom.: 569

Bravo AF: 0.203

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743836; hg19: chr3-52260782;