chr10-122902204-T-G

Variant names:

• chr10-122902204-T-G
• rs12354676

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 0.0142 in 152,248 control chromosomes in the GnomAD database, including 31 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 0.014 (31 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0623 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: 0.0142 AC: 2162 AN: 152130 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.00323

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0167

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.00907

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

GnomAD4 genome AF: 0.0142 AC: 2163 AN: 152248 Hom.: 31 Cov.: 32 AF XY: 0.0143 AC XY: 1061 AN XY: 74418

African (AFR) AF: 0.00322 AC: 134 AN: 41572

American (AMR) AF: 0.0167 AC: 256 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3468

East Asian (EAS) AF: 0.0681 AC: 352 AN: 5168

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4822

European-Finnish (FIN) AF: 0.00989 AC: 105 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0174 AC: 1183 AN: 68000

Other (OTH) AF: 0.00898 AC: 19 AN: 2116

Alfa AF: 0.00709 Hom.: 1

Bravo AF: 0.0149

Asia WGS AF: 0.0320 AC: 111 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	5.4
DANN	Benign	0.34
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs12354676; hg19: chr10-124661720;