3-3428776-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455703.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223727	ENST00000420000.6	TSL:4	n.201-46126G>A		intron	N/A
	ENSG00000223727	ENST00000451031.5	TSL:3	n.175+12132G>A		intron	N/A
	ENSG00000223727	ENST00000455703.1	TSL:2	n.60-46126G>A		intron	N/A

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

African (AFR) AF: 0.0252 AC: 1045 AN: 41518

American (AMR) AF: 0.0812 AC: 1242 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1218 AN: 5164

South Asian (SAS) AF: 0.0690 AC: 332 AN: 4814

European-Finnish (FIN) AF: 0.0368 AC: 389 AN: 10580

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1732 AN: 68012

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0378 Hom.: 32

Bravo AF: 0.0437

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.64

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17031343;

hg19: chr3-3470460;