10-116055375-G-A

Variant names:

• chr10-116055375-G-A
• rs180557

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 0.232 in 152,086 control chromosomes in the GnomAD database, including 4,903 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 0.23 (4903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.232 AC: 35298 AN: 151968 Hom.: 4894 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.232 AC: 35342 AN: 152086 Hom.: 4903 Cov.: 32 AF XY: 0.230 AC XY: 17118 AN XY: 74348

African (AFR) AF: 0.391 AC: 16197 AN: 41466

American (AMR) AF: 0.166 AC: 2532 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3470

East Asian (EAS) AF: 0.133 AC: 689 AN: 5182

South Asian (SAS) AF: 0.156 AC: 751 AN: 4822

European-Finnish (FIN) AF: 0.186 AC: 1964 AN: 10566

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.177 AC: 12046 AN: 67980

Other (OTH) AF: 0.228 AC: 482 AN: 2112

Alfa AF: 0.162 Hom.: 446

Bravo AF: 0.235

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.18
DANN	Benign	0.59
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs180557; hg19: chr10-117814886;