rs11202308

chr10-87039853-T-G

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 0.113 in 152,266 control chromosomes in the GnomAD database, including 1,254 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 0.11 (1254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 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: 0.113 AC: 17183 AN: 152148 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.113 AC: 17172 AN: 152266 Hom.: 1254 Cov.: 32 AF XY: 0.113 AC XY: 8444 AN XY: 74458

Gnomad4 AFR AF: 0.0257

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.0665

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.147

Alfa AF: 0.143 Hom.: 1138

Bravo AF: 0.112

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.5
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11202308; hg19: chr10-88799610;