chr3-86206522-T-C

Variant names:

• chr3-86206522-T-C
• rs7428796
• ENST00000722615.1:n.682-589A>G

Variant summary

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

The ENST00000722615.1(ENSG00000239767):​n.682-589A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,556 control chromosomes in the GnomAD database, including 20,761 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 0.51 (20761 hom., cov: 29)
• Consequence: ENSG00000239767 ENST00000722615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 7 publications found

Genes affected

ENSG00000239767 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722615.1. 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
	LOC102723364	NR_188544.1		n.680-589A>G		intron	N/A
	LOC102723364	NR_188545.1		n.598-589A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000239767	ENST00000722615.1		n.682-589A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76636 AN: 151440 Hom.: 20760 Cov.: 29

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.506 AC: 76661 AN: 151556 Hom.: 20761 Cov.: 29 AF XY: 0.504 AC XY: 37315 AN XY: 74050

African (AFR) AF: 0.313 AC: 12912 AN: 41302

American (AMR) AF: 0.510 AC: 7752 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1793 AN: 3464

East Asian (EAS) AF: 0.436 AC: 2232 AN: 5114

South Asian (SAS) AF: 0.435 AC: 2088 AN: 4804

European-Finnish (FIN) AF: 0.649 AC: 6858 AN: 10566

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41301 AN: 67822

Other (OTH) AF: 0.522 AC: 1093 AN: 2094

Alfa AF: 0.575 Hom.: 83395

Bravo AF: 0.489

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7428796; hg19: chr3-86255672;