10-129228428-T-G

Variant names:

• chr10-129228428-T-G
• rs1861860

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 0.176 in 152,220 control chromosomes in the GnomAD database, including 2,510 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 0.18 (2510 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 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: 0.176 AC: 26796 AN: 152100 Hom.: 2511 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.176 AC: 26803 AN: 152220 Hom.: 2510 Cov.: 33 AF XY: 0.179 AC XY: 13341 AN XY: 74428

African (AFR) AF: 0.127 AC: 5274 AN: 41530

American (AMR) AF: 0.196 AC: 2995 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1132 AN: 5178

South Asian (SAS) AF: 0.300 AC: 1449 AN: 4828

European-Finnish (FIN) AF: 0.215 AC: 2279 AN: 10596

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12547 AN: 67996

Other (OTH) AF: 0.172 AC: 364 AN: 2116

Alfa AF: 0.179 Hom.: 1104

Bravo AF: 0.171

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.67
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1861860; hg19: chr10-131026692;