10-57557163-C-G

Variant names:

• chr10-57557163-C-G
• rs35866326

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 0.139 in 151,892 control chromosomes in the GnomAD database, including 1,769 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 0.14 (1769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20981 AN: 151774 Hom.: 1750 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0707

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.139 AC: 21040 AN: 151892 Hom.: 1769 Cov.: 32 AF XY: 0.141 AC XY: 10483 AN XY: 74254

African (AFR) AF: 0.176 AC: 7310 AN: 41476

American (AMR) AF: 0.243 AC: 3694 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0707 AC: 245 AN: 3466

East Asian (EAS) AF: 0.190 AC: 979 AN: 5154

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4820

European-Finnish (FIN) AF: 0.0516 AC: 547 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0979 AC: 6639 AN: 67842

Other (OTH) AF: 0.157 AC: 332 AN: 2108

Alfa AF: 0.114 Hom.: 160

Bravo AF: 0.152

Asia WGS AF: 0.273 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs35866326; hg19: chr10-59316923;