rs360929

Variant names:

• chr4-151986548-G-A
• rs360929
• ENST00000652265.1:n.1354+4024C>T

Variant summary

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

The ENST00000652265.1(ENSG00000286066):​n.1354+4024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,138 control chromosomes in the GnomAD database, including 46,356 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 0.78 (46356 hom., cov: 33)
• Consequence: ENSG00000286066 ENST00000652265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 10 publications found

Genes affected

ENSG00000286066 (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 (NFE) allele frequency at 95% confidence interval = 0.843 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
ENSG00000286066	ENST00000652265.1	n.1354+4024C>T		intron_variant	Intron 1 of 1
ENSG00000286066	ENST00000731965.1	n.210+5174C>T		intron_variant	Intron 1 of 1
ENSG00000286066	ENST00000731966.1	n.374+4206C>T		intron_variant	Intron 2 of 2
ENSG00000286066	ENST00000731967.1	n.1343+4024C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117997 AN: 152020 Hom.: 46337 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.776 AC: 118073 AN: 152138 Hom.: 46356 Cov.: 33 AF XY: 0.770 AC XY: 57242 AN XY: 74364

African (AFR) AF: 0.659 AC: 27358 AN: 41502

American (AMR) AF: 0.815 AC: 12455 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3727 AN: 5172

South Asian (SAS) AF: 0.714 AC: 3435 AN: 4810

European-Finnish (FIN) AF: 0.732 AC: 7748 AN: 10580

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57711 AN: 68006

Other (OTH) AF: 0.809 AC: 1711 AN: 2116

Alfa AF: 0.824 Hom.: 116493

Bravo AF: 0.781

Asia WGS AF: 0.708 AC: 2464 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	2.7
DANN	Benign	0.32
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs360929; hg19: chr4-152907700;