rs10505417

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000254303 (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 (AMR) allele frequency at 95% confidence interval = 0.0664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523792.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254303	ENST00000523792.1	TSL:1	n.160+26494G>A		intron	N/A
	ENSG00000254303	ENST00000770642.1		n.122+26494G>A		intron	N/A

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

African (AFR) AF: 0.00489 AC: 203 AN: 41520

American (AMR) AF: 0.0699 AC: 1066 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.0366 AC: 189 AN: 5168

South Asian (SAS) AF: 0.00644 AC: 31 AN: 4810

European-Finnish (FIN) AF: 0.00340 AC: 36 AN: 10584

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0120 AC: 818 AN: 67998

Other (OTH) AF: 0.0180 AC: 38 AN: 2112

Alfa AF: 0.0172 Hom.: 34

Bravo AF: 0.0244

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.80
PhyloP100		-0.95

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10505417;

hg19: chr8-123112770;