chr3-52227015-A-G

Variant names:

• chr3-52227015-A-G
• rs187084
• ENST00000494383.1:c.462+2646T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494383.1(ENSG00000173366):​c.462+2646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,132 control chromosomes in the GnomAD database, including 11,169 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 0.38 (11169 hom., cov: 33)
• Consequence: ENSG00000173366 ENST00000494383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

Genes affected

ENSG00000173366 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 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.462+2646T>C		intron_variant	Intron 4 of 4	2		ENSP00000417517.1
ENSG00000173366	ENST00000478201.1	n.112-1380T>C		intron_variant	Intron 1 of 2	2		ENSP00000419980.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57423 AN: 152014 Hom.: 11156 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.378 AC: 57464 AN: 152132 Hom.: 11169 Cov.: 33 AF XY: 0.379 AC XY: 28156 AN XY: 74384

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.369

Alfa AF: 0.401 Hom.: 12450

Bravo AF: 0.375

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.36

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: rs187084; hg19: chr3-52261031;