rs10505417

Variant names:

• chr8-122100531-C-T
• rs10505417
• ENST00000523792.1:n.160+26494G>A

Variant summary

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

The ENST00000523792.1(ENSG00000254303):​n.160+26494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0157 in 152,126 control chromosomes in the GnomAD database, including 64 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 0.016 (64 hom., cov: 32)
• Consequence: ENSG00000254303 ENST00000523792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947

Genes affected

ENSG00000254303 (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 (AMR) allele frequency at 95% confidence interval = 0.0664 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
ENSG00000254303	ENST00000523792.1	n.160+26494G>A		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0156 AC: 2378 AN: 152008 Hom.: 62 Cov.: 32

Gnomad AFR AF: 0.00490

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.00623

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0157 AC: 2384 AN: 152126 Hom.: 64 Cov.: 32 AF XY: 0.0160 AC XY: 1190 AN XY: 74366

Gnomad4 AFR AF: 0.00489

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.0366

Gnomad4 SAS AF: 0.00644

Gnomad4 FIN AF: 0.00340

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0217 Hom.: 21

Bravo AF: 0.0244

Asia WGS AF: 0.0180 AC: 61 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	0.84
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505417; hg19: chr8-123112770;