3-19638916-C-T

Variant names:

• chr3-19638916-C-T
• rs2203428
• ENST00000670571.1:n.512-22863G>A

Variant summary

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

The ENST00000670571.1(ENSG00000287069):​n.512-22863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,904 control chromosomes in the GnomAD database, including 4,052 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 0.18 (4052 hom., cov: 32)
• Consequence: ENSG00000287069 ENST00000670571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

ENSG00000287069 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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
ENSG00000287069	ENST00000670571.1	n.512-22863G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28037 AN: 151786 Hom.: 4040 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.185 AC: 28095 AN: 151904 Hom.: 4052 Cov.: 32 AF XY: 0.185 AC XY: 13704 AN XY: 74250

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.0831

Gnomad4 OTH AF: 0.175

Alfa AF: 0.103 Hom.: 604

Bravo AF: 0.204

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203428; hg19: chr3-19680408;