8-63396283-A-G

Variant names:

• chr8-63396283-A-G
• rs7007978
• ENST00000517829.1:n.457-10377T>C

Variant summary

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

The ENST00000517829.1(ENSG00000253205):​n.457-10377T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,134 control chromosomes in the GnomAD database, including 45,009 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 0.76 (45009 hom., cov: 33)
• Consequence: ENSG00000253205 ENST00000517829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 0 publications found

Genes affected

ENSG00000253205 (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 = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517829.1. 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
	LOC105375875	NR_188106.1		n.1021-10377T>C		intron	N/A
	LOC105375875	NR_188107.1		n.687-10377T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253205	ENST00000517829.1	TSL:3	n.457-10377T>C		intron	N/A
	ENSG00000253205	ENST00000519819.5	TSL:3	n.135-10377T>C		intron	N/A
	ENSG00000253205	ENST00000521221.6	TSL:2	n.729-10377T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116050 AN: 152016 Hom.: 44949 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.764 AC: 116171 AN: 152134 Hom.: 45009 Cov.: 33 AF XY: 0.766 AC XY: 56993 AN XY: 74374

African (AFR) AF: 0.886 AC: 36786 AN: 41512

American (AMR) AF: 0.806 AC: 12334 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3472

East Asian (EAS) AF: 0.926 AC: 4793 AN: 5174

South Asian (SAS) AF: 0.861 AC: 4150 AN: 4822

European-Finnish (FIN) AF: 0.660 AC: 6977 AN: 10574

Middle Eastern (MID) AF: 0.652 AC: 189 AN: 290

European-Non Finnish (NFE) AF: 0.683 AC: 46425 AN: 67972

Other (OTH) AF: 0.768 AC: 1624 AN: 2114

Alfa AF: 0.723 Hom.: 5637

Bravo AF: 0.779

Asia WGS AF: 0.892 AC: 3101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.83
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7007978; hg19: chr8-64308841;