rs10500777

Positions:

• chr11-13254764-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 0.154 in 152,090 control chromosomes in the GnomAD database, including 1,923 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 0.15 (1923 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23371 AN: 151972 Hom.: 1919 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.154 AC: 23392 AN: 152090 Hom.: 1923 Cov.: 33 AF XY: 0.159 AC XY: 11789 AN XY: 74330

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.153

Alfa AF: 0.147 Hom.: 208

Bravo AF: 0.151

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500777; hg19: chr11-13276311;