chr10-83752139-C-T

Variant names:

• chr10-83752139-C-T
• rs11200394

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 0.0775 in 152,222 control chromosomes in the GnomAD database, including 567 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 0.077 (567 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11781 AN: 152104 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0982

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0775 AC: 11792 AN: 152222 Hom.: 567 Cov.: 33 AF XY: 0.0784 AC XY: 5832 AN XY: 74416

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0572

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0982

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0452 Hom.: 60

Bravo AF: 0.0704

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.0
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11200394; hg19: chr10-85511895;