8-93980339-C-G

Variant names:

• chr8-93980339-C-G
• rs4397372
• ENST00000804453.1:n.128-18364C>G

Variant summary

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

The ENST00000804453.1(ENSG00000304545):​n.128-18364C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,964 control chromosomes in the GnomAD database, including 29,470 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 0.60 (29470 hom., cov: 32)
• Consequence: ENSG00000304545 ENST00000804453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 1 publications found

Genes affected

ENSG00000304545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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
ENSG00000304545	ENST00000804453.1	n.128-18364C>G		intron_variant	Intron 1 of 1
ENSG00000304545	ENST00000804454.1	n.27-18364C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90450 AN: 151846 Hom.: 29408 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.596 AC: 90567 AN: 151964 Hom.: 29470 Cov.: 32 AF XY: 0.597 AC XY: 44358 AN XY: 74260

African (AFR) AF: 0.833 AC: 34559 AN: 41470

American (AMR) AF: 0.650 AC: 9922 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4706 AN: 5176

South Asian (SAS) AF: 0.572 AC: 2756 AN: 4820

European-Finnish (FIN) AF: 0.414 AC: 4356 AN: 10532

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

European-Non Finnish (NFE) AF: 0.451 AC: 30660 AN: 67920

Other (OTH) AF: 0.588 AC: 1240 AN: 2108

Alfa AF: 0.328 Hom.: 726

Bravo AF: 0.627

Asia WGS AF: 0.758 AC: 2637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.73
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4397372; hg19: chr8-94992567;