rs79323383

Variant names:

• chr8-120839185-T-G
• rs79323383
• ENST00000787995.1:n.241+12115T>G

Variant summary

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

The ENST00000787995.1(ENSG00000302591):​n.241+12115T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,230 control chromosomes in the GnomAD database, including 422 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 0.050 (422 hom., cov: 32)
• Consequence: ENSG00000302591 ENST00000787995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 1 publications found

Genes affected

ENSG00000302591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787995.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302591	ENST00000787995.1		n.241+12115T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0498 AC: 7574 AN: 152112 Hom.: 415 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0260

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0499 AC: 7595 AN: 152230 Hom.: 422 Cov.: 32 AF XY: 0.0545 AC XY: 4060 AN XY: 74454

African (AFR) AF: 0.0267 AC: 1108 AN: 41552

American (AMR) AF: 0.152 AC: 2323 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.169 AC: 873 AN: 5174

South Asian (SAS) AF: 0.121 AC: 585 AN: 4822

European-Finnish (FIN) AF: 0.0312 AC: 331 AN: 10612

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0260 AC: 1771 AN: 68000

Other (OTH) AF: 0.0710 AC: 150 AN: 2114

Alfa AF: 0.0368 Hom.: 351

Bravo AF: 0.0598

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.60
DANN	Benign	0.71
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs79323383; hg19: chr8-121851425;