rs1746048

chr10-44280376-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.241

Alfa AF: 0.167 Hom.: 4076

Bravo AF: 0.265

Asia WGS AF: 0.325 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1746048; hg19: chr10-44775824;