rs10505407

Variant names:

• chr8-121498201-A-G
• rs10505407
• ENST00000784704.1:n.285+24994A>G

Variant summary

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

The ENST00000784704.1(ENSG00000302156):​n.285+24994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 152,204 control chromosomes in the GnomAD database, including 748 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 0.072 (748 hom., cov: 32)
• Consequence: ENSG00000302156 ENST00000784704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 1 publications found

Genes affected

ENSG00000302156 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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
ENSG00000302156	ENST00000784704.1	n.285+24994A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10892 AN: 152088 Hom.: 742 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0283

Gnomad FIN AF: 0.00490

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0718 AC: 10925 AN: 152204 Hom.: 748 Cov.: 32 AF XY: 0.0715 AC XY: 5322 AN XY: 74436

African (AFR) AF: 0.176 AC: 7303 AN: 41488

American (AMR) AF: 0.0703 AC: 1076 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 181 AN: 3472

East Asian (EAS) AF: 0.0342 AC: 177 AN: 5178

South Asian (SAS) AF: 0.0282 AC: 136 AN: 4830

European-Finnish (FIN) AF: 0.00490 AC: 52 AN: 10604

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0265 AC: 1801 AN: 68014

Other (OTH) AF: 0.0619 AC: 131 AN: 2116

Alfa AF: 0.0372 Hom.: 395

Bravo AF: 0.0811

Asia WGS AF: 0.0650 AC: 226 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	0.47
DANN	Benign	0.33
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10505407; hg19: chr8-122510441;