chr3-3428776-C-T

Variant names:

• chr3-3428776-C-T
• rs17031343
• ENST00000420000.6:n.201-46126G>A

Variant summary

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

The ENST00000455703.1(ENSG00000223727):​n.60-46126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 152,172 control chromosomes in the GnomAD database, including 293 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 0.040 (293 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000455703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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
ENSG00000223727	ENST00000420000.6	n.201-46126G>A		intron_variant	Intron 2 of 4	4
ENSG00000223727	ENST00000451031.5	n.175+12132G>A		intron_variant	Intron 2 of 5	3
ENSG00000223727	ENST00000455703.1	n.60-46126G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6075 AN: 152054 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0399 AC: 6074 AN: 152172 Hom.: 293 Cov.: 32 AF XY: 0.0425 AC XY: 3158 AN XY: 74390

Gnomad4 AFR AF: 0.0252

Gnomad4 AMR AF: 0.0812

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.0690

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0380 Hom.: 32

Bravo AF: 0.0437

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17031343; hg19: chr3-3470460;