rs10503564

Variant names:

• chr8-15948825-C-T
• rs10503564
• ENST00000664439.1:n.163+16520G>A

Variant summary

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

The ENST00000664439.1(ENSG00000287476):​n.163+16520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0919 in 152,188 control chromosomes in the GnomAD database, including 1,439 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 0.092 (1439 hom., cov: 33)
• Consequence: ENSG00000287476 ENST00000664439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 2 publications found

Genes affected

ENSG00000287476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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
ENSG00000287476	ENST00000664439.1	n.163+16520G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13941 AN: 152070 Hom.: 1429 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0773

Gnomad FIN AF: 0.00886

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0919 AC: 13988 AN: 152188 Hom.: 1439 Cov.: 33 AF XY: 0.0913 AC XY: 6794 AN XY: 74404

African (AFR) AF: 0.240 AC: 9967 AN: 41474

American (AMR) AF: 0.127 AC: 1935 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.149 AC: 773 AN: 5172

South Asian (SAS) AF: 0.0765 AC: 369 AN: 4824

European-Finnish (FIN) AF: 0.00886 AC: 94 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 684 AN: 68022

Other (OTH) AF: 0.0690 AC: 146 AN: 2116

Alfa AF: 0.0467 Hom.: 128

Bravo AF: 0.110

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.44
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10503564; hg19: chr8-15806334;