rs796720

Variant names:

• chr12-53865825-A-G
• rs796720
• ENST00000652339.1:n.509+4947A>G

Variant summary

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

The ENST00000652339.1(ENSG00000286069):​n.509+4947A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,150 control chromosomes in the GnomAD database, including 61,381 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 0.89 (61381 hom., cov: 31)
• Consequence: ENSG00000286069 ENST00000652339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 2 publications found

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652339.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105378250	NR_189097.1		n.398+15413A>G		intron	N/A
	LOC105378250	NR_189098.1		n.497-9330A>G		intron	N/A
	LOC105378250	NR_189099.1		n.591+4947A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286069	ENST00000652339.1		n.509+4947A>G		intron	N/A
	ENSG00000286069	ENST00000654713.2		n.317+15413A>G		intron	N/A
	ENSG00000286069	ENST00000656247.1		n.344+15413A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135170 AN: 152032 Hom.: 61350 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.889 AC: 135241 AN: 152150 Hom.: 61381 Cov.: 31 AF XY: 0.879 AC XY: 65362 AN XY: 74368

African (AFR) AF: 0.908 AC: 37675 AN: 41510

American (AMR) AF: 0.744 AC: 11360 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3298 AN: 3470

East Asian (EAS) AF: 0.339 AC: 1747 AN: 5156

South Asian (SAS) AF: 0.836 AC: 4028 AN: 4820

European-Finnish (FIN) AF: 0.865 AC: 9158 AN: 10582

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.954 AC: 64910 AN: 68018

Other (OTH) AF: 0.891 AC: 1884 AN: 2114

Alfa AF: 0.892 Hom.: 24731

Bravo AF: 0.879

Asia WGS AF: 0.622 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs796720; hg19: chr12-54259609;