rs10504152

Positions:

• chr8-53217555-G-A
• chr8-53217555-G-C
• chr8-53217555-G-T

Variant summary

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

The ENST00000524425.1(ENSG00000254687):​n.670+1051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,998 control chromosomes in the GnomAD database, including 3,654 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 0.20 (3654 hom., cov: 32)
• Consequence: ENSG00000254687 ENST00000524425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

ENSG00000254687 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375836	NR_188096.1	n.639+1051G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254687	ENST00000524425.1	n.670+1051G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29996 AN: 151882 Hom.: 3648 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.198 AC: 30033 AN: 151998 Hom.: 3654 Cov.: 32 AF XY: 0.195 AC XY: 14476 AN XY: 74304

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0713

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.191

Alfa AF: 0.0925 Hom.: 175

Bravo AF: 0.216

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504152; hg19: chr8-54130115;