8-114015721-A-G

Variant names:

• chr8-114015721-A-G
• rs1397966
• ENST00000768477.1:n.327+9399A>G

Variant summary

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

The ENST00000768477.1(ENSG00000300059):​n.327+9399A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,038 control chromosomes in the GnomAD database, including 9,764 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 0.35 (9764 hom., cov: 33)
• Consequence: ENSG00000300059 ENST00000768477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 5 publications found

Genes affected

ENSG00000300059 (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 (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768477.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300059	ENST00000768477.1		n.327+9399A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53344 AN: 151920 Hom.: 9764 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.351 AC: 53352 AN: 152038 Hom.: 9764 Cov.: 33 AF XY: 0.347 AC XY: 25769 AN XY: 74328

African (AFR) AF: 0.258 AC: 10685 AN: 41488

American (AMR) AF: 0.379 AC: 5775 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1184 AN: 3466

East Asian (EAS) AF: 0.170 AC: 877 AN: 5174

South Asian (SAS) AF: 0.355 AC: 1713 AN: 4826

European-Finnish (FIN) AF: 0.348 AC: 3679 AN: 10576

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28096 AN: 67946

Other (OTH) AF: 0.371 AC: 784 AN: 2114

Alfa AF: 0.372 Hom.: 5518

Bravo AF: 0.347

Asia WGS AF: 0.299 AC: 1040 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	6.3
DANN	Benign	0.52
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1397966; hg19: chr8-115027950;