rs10517058

Variant names:

• chr4-42871198-A-G
• rs10517058

Variant summary

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

The variant allele was found at a frequency of 0.0369 in 152,218 control chromosomes in the GnomAD database, including 190 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 0.037 (190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0825 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

Frequencies

GnomAD3 genomes AF: 0.0369 AC: 5606 AN: 152100 Hom.: 190 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0369 AC: 5614 AN: 152218 Hom.: 190 Cov.: 32 AF XY: 0.0370 AC XY: 2756 AN XY: 74418

African (AFR) AF: 0.0849 AC: 3526 AN: 41544

American (AMR) AF: 0.0188 AC: 288 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3468

East Asian (EAS) AF: 0.0298 AC: 154 AN: 5172

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4822

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0162 AC: 1102 AN: 68004

Other (OTH) AF: 0.0308 AC: 65 AN: 2112

Alfa AF: 0.0265 Hom.: 36

Bravo AF: 0.0379

Asia WGS AF: 0.0510 AC: 176 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.71
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10517058; hg19: chr4-42873215;