rs11252845

chr10-4951623-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 0.0411 in 152,250 control chromosomes in the GnomAD database, including 208 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 0.041 (208 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0579 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: 0.0412 AC: 6263 AN: 152132 Hom.: 208 Cov.: 33

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0411 AC: 6258 AN: 152250 Hom.: 208 Cov.: 33 AF XY: 0.0392 AC XY: 2918 AN XY: 74440

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0183

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0595

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0533 Hom.: 126

Bravo AF: 0.0421

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.69
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11252845; hg19: chr10-4993815;