10-69441748-C-T

Variant names:

• chr10-69441748-C-T
• rs12242391

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 0.108 in 152,240 control chromosomes in the GnomAD database, including 986 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 0.11 (986 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16359 AN: 152122 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00595

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.108 AC: 16376 AN: 152240 Hom.: 986 Cov.: 32 AF XY: 0.105 AC XY: 7828 AN XY: 74424

African (AFR) AF: 0.0873 AC: 3625 AN: 41526

American (AMR) AF: 0.101 AC: 1537 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3470

East Asian (EAS) AF: 0.00616 AC: 32 AN: 5194

South Asian (SAS) AF: 0.0653 AC: 315 AN: 4824

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10596

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8782 AN: 68020

Other (OTH) AF: 0.102 AC: 216 AN: 2114

Alfa AF: 0.114 Hom.: 1269

Bravo AF: 0.107

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.51
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs12242391; hg19: chr10-71201504;