rs10457252

Variant names:

• chr6-112823582-T-C
• rs10457252
• XR_001744300.1:n.59+23180A>G

Variant summary

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

The XR_001744300.1(LOC107986634):​n.59+23180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,048 control chromosomes in the GnomAD database, including 5,459 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 0.25 (5459 hom., cov: 32)
• Consequence: LOC107986634 XR_001744300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 3 publications found

Genes affected

LOC107986634 (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 (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37685 AN: 151930 Hom.: 5456 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0710

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.248 AC: 37704 AN: 152048 Hom.: 5459 Cov.: 32 AF XY: 0.251 AC XY: 18642 AN XY: 74336

African (AFR) AF: 0.120 AC: 4994 AN: 41512

American (AMR) AF: 0.192 AC: 2932 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3468

East Asian (EAS) AF: 0.0709 AC: 366 AN: 5160

South Asian (SAS) AF: 0.313 AC: 1512 AN: 4828

European-Finnish (FIN) AF: 0.405 AC: 4279 AN: 10570

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21587 AN: 67920

Other (OTH) AF: 0.238 AC: 503 AN: 2114

Alfa AF: 0.289 Hom.: 9436

Bravo AF: 0.223

Asia WGS AF: 0.185 AC: 645 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	3.5
DANN	Benign	0.76
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs10457252; hg19: chr6-113144784;