8-63396283-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521221.6(ENSG00000253205):​n.729-10377T>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 ENST00000521221.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

Genes affected

ENSG00000253205 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375875	NR_188106.1	n.1021-10377T>C		intron_variant	Intron 4 of 4
LOC105375875	NR_188107.1	n.687-10377T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253205	ENST00000517829.1	n.457-10377T>C		intron_variant	Intron 3 of 3	3
ENSG00000253205	ENST00000519819.5	n.135-10377T>C		intron_variant	Intron 2 of 2	3
ENSG00000253205	ENST00000521221.6	n.729-10377T>C		intron_variant	Intron 3 of 3	2

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

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.768

Alfa AF: 0.717 Hom.: 5335

Bravo AF: 0.779

Asia WGS AF: 0.892 AC: 3101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7007978; hg19: chr8-64308841;