10-63048233-T-C

Variant names:

• chr10-63048233-T-C
• rs7903145

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 0.151 in 152,006 control chromosomes in the GnomAD database, including 2,091 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 0.15 (2091 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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: 0.151 AC: 22941 AN: 151888 Hom.: 2093 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0684

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.151 AC: 22959 AN: 152006 Hom.: 2091 Cov.: 31 AF XY: 0.149 AC XY: 11102 AN XY: 74326

African (AFR) AF: 0.249 AC: 10319 AN: 41416

American (AMR) AF: 0.149 AC: 2268 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5186

South Asian (SAS) AF: 0.238 AC: 1143 AN: 4800

European-Finnish (FIN) AF: 0.0684 AC: 724 AN: 10588

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7326 AN: 67972

Other (OTH) AF: 0.155 AC: 326 AN: 2108

Alfa AF: 0.125 Hom.: 183

Bravo AF: 0.159

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.5
DANN	Benign	0.84
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7903145; hg19: chr10-64807993;