10-44477206-C-G

Variant names:

• chr10-44477206-C-G
• rs1147962

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 0.155 in 152,268 control chromosomes in the GnomAD database, including 1,975 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 0.16 (1975 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 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: 0.155 AC: 23644 AN: 152150 Hom.: 1973 Cov.: 34

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.155 AC: 23658 AN: 152268 Hom.: 1975 Cov.: 34 AF XY: 0.154 AC XY: 11446 AN XY: 74458

African (AFR) AF: 0.0849 AC: 3529 AN: 41556

American (AMR) AF: 0.133 AC: 2039 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1200 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1663 AN: 10610

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12895 AN: 68012

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.159 Hom.: 264

Bravo AF: 0.150

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.65
DANN	Benign	0.58
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1147962; hg19: chr10-44972654;