ENST00000724020.1:n.163-9281C>G

Variant names:

• chr4-186811057-C-G
• rs323421
• ENST00000724020.1:n.163-9281C>G

Variant summary

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

The ENST00000724020.1(ENSG00000294511):​n.163-9281C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,048 control chromosomes in the GnomAD database, including 17,800 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 0.46 (17800 hom., cov: 32)
• Consequence: ENSG00000294511 ENST00000724020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 1 publications found

Genes affected

ENSG00000294511 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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
ENSG00000294511	ENST00000724020.1	n.163-9281C>G		intron_variant	Intron 1 of 1
ENSG00000294511	ENST00000724021.1	n.206+8160C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70362 AN: 151930 Hom.: 17789 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.463 AC: 70419 AN: 152048 Hom.: 17800 Cov.: 32 AF XY: 0.460 AC XY: 34198 AN XY: 74320

African (AFR) AF: 0.688 AC: 28559 AN: 41486

American (AMR) AF: 0.319 AC: 4874 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2171 AN: 5176

South Asian (SAS) AF: 0.403 AC: 1937 AN: 4810

European-Finnish (FIN) AF: 0.382 AC: 4035 AN: 10558

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26012 AN: 67968

Other (OTH) AF: 0.421 AC: 888 AN: 2108

Alfa AF: 0.415 Hom.: 1738

Bravo AF: 0.468

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.45
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs323421; hg19: chr4-187732211;