rs1746048

Variant names:

• chr10-44280376-C-T
• rs1746048

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 0.251 in 152,108 control chromosomes in the GnomAD database, including 6,362 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 0.25 (6362 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 148 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 = 0.457 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: 0.250 AC: 38052 AN: 151988 Hom.: 6335 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.251 AC: 38134 AN: 152108 Hom.: 6362 Cov.: 33 AF XY: 0.253 AC XY: 18819 AN XY: 74354

African (AFR) AF: 0.463 AC: 19187 AN: 41470

American (AMR) AF: 0.227 AC: 3472 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5162

South Asian (SAS) AF: 0.351 AC: 1691 AN: 4816

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10584

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9154 AN: 68002

Other (OTH) AF: 0.241 AC: 508 AN: 2110

Alfa AF: 0.178 Hom.: 11053

Bravo AF: 0.265

Asia WGS AF: 0.325 AC: 1132 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	7.9
DANN	Benign	0.79
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1746048; hg19: chr10-44775824;