rs17684824

Variant names:

• chr3-3546358-A-C
• rs17684824
• ENST00000420000.6:n.200+80386T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420000.6(ENSG00000223727):​n.200+80386T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,082 control chromosomes in the GnomAD database, including 997 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 0.10 (997 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420000.6. 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.200+80386T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15244 AN: 151964 Hom.: 999 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.100 AC: 15244 AN: 152082 Hom.: 997 Cov.: 32 AF XY: 0.101 AC XY: 7534 AN XY: 74314

African (AFR) AF: 0.0235 AC: 977 AN: 41562

American (AMR) AF: 0.122 AC: 1865 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 313 AN: 3462

East Asian (EAS) AF: 0.164 AC: 847 AN: 5172

South Asian (SAS) AF: 0.136 AC: 657 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1504 AN: 10560

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8714 AN: 67900

Other (OTH) AF: 0.0990 AC: 209 AN: 2112

Alfa AF: 0.121 Hom.: 1270

Bravo AF: 0.0984

Asia WGS AF: 0.113 AC: 393 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.35
PhyloP100		1.3

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: rs17684824;

hg19: chr3-3588042;