rs1746049

chr10-44280862-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 0.223 in 152,058 control chromosomes in the GnomAD database, including 5,578 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 0.22 (5578 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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: 0.223 AC: 33912 AN: 151940 Hom.: 5555 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0334

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.223 AC: 33979 AN: 152058 Hom.: 5578 Cov.: 33 AF XY: 0.220 AC XY: 16390 AN XY: 74340

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0332

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.219

Alfa AF: 0.210 Hom.: 897

Bravo AF: 0.232

Asia WGS AF: 0.182 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.18
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1746049; hg19: chr10-44776310;