rs2280450

chr10-124747710-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 0.445 in 152,082 control chromosomes in the GnomAD database, including 17,922 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 0.44 (17922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 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: 0.445 AC: 67638 AN: 151964 Hom.: 17904 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.445 AC: 67662 AN: 152082 Hom.: 17922 Cov.: 33 AF XY: 0.452 AC XY: 33576 AN XY: 74334

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.480

Alfa AF: 0.522 Hom.: 4491

Bravo AF: 0.426

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	13
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2280450; hg19: chr10-126436279;